BLAST Search Results

# HG changeset patch # User peterjc # Date 1422624448 18000 # Node ID 432ea9614cc958ec2d64f2a2abc17ec0cdbec9ab Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc diff -r 000000000000 -r 432ea9614cc9 test-data/blastdb.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb.loc Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,7 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of nucleotide BLAST databases used in functional +# tests for blastn etc. +# +# See the file tool-data/blastdb.loc.sample for more information. +# +three_human_mRNA Three Human mRNAs ${__HERE__}/three_human_mRNA.fasta diff -r 000000000000 -r 432ea9614cc9 test-data/blastdb_d.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb_d.loc Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,7 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of protein domain BLAST databases used in functional +# tests of rpsblast etc. +# +# See the file tool-data/blastdb_d.loc.sample for more information. +# +cd00003_and_cd00008 Domains CD00003 (PNPsynthase) and CD00008 (PIN_53EXO-like) ${__HERE__}/cd00003_and_cd00008 diff -r 000000000000 -r 432ea9614cc9 test-data/blastdb_p.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastdb_p.loc Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,8 @@ +# This is a test file distributed with the Galaxy BLAST+ wrapper for +# defining a list of protein BLAST databases used in functional tests +# for blastp etc. +# +# See the file tool-data/blastdb_p.loc.sample for more information. +# +four_human_proteins Four Human Proteins (no taxid) ${__HERE__}/four_human_proteins.fasta +four_human_proteins_taxid Four Human Proteins (with taxid) ${__HERE__}/four_human_proteins_taxid.fasta diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_arabidopsis.extended.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_arabidopsis.extended.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,1 @@ +chunk_of_plant chrIII 100.00 630 0 0 1 630 4341 4970 0.0 1164 chrIII 630 630 630 0 100.00 1 1 GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT 630 23459830 gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_arabidopsis.standard.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_arabidopsis.standard.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,1 @@ +chunk_of_plant chrIII 100.00 630 0 0 1 630 4341 4970 0.0 1164 diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_arabidopsis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_arabidopsis.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,71 @@ + + + + blastn + BLASTN 2.2.28+ + Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. + /mnt/galaxy/galaxy-central/database/files/000/dataset_857_files/blastdb + Query_1 + chunk_of_plant + 630 + + + 0.001 + 1 + -2 + 0 + 0 + L;m; + + + + + 1 + Query_1 + chunk_of_plant + 630 + + + 1 + gnl|BL_ORD_ID|2 + chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence + 2 + 23459830 + + + 1 + 1164.51 + 630 + 0 + 1 + 630 + 4341 + 4970 + 1 + 1 + 630 + 630 + 0 + 630 + GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT + GATGTTCAATACTGTTTCCAACAAAAAGATTGTTGTCCTCGAGTTCGCCTTCAAGAAAGACACGAGAGAGACTCCAGCCATTGACGTCTGCAAAGGTTTGTTAGGAGACAAGGCCCGAATCAGCATCTATGATCCACAAGTCACGGAAGAACAAATCCAAAGAGACTTAACCATGAACACATTCGACTGGGACCATCCACTTCACCTCCAACCCATGAGTCCAACCACTGTGAAACAAGTCTCAGTTGCTTGGGACGCTTACGCTGCCACCAAAGACGCCCACGGAATCTGCTTGTTAACCGAGTGGGACGAGTATAAGACGCTTGACTATGAGCGGATTTTTGAAAACATGCAGAAACCAGCGTTTGTCTTCGATGGCAGAAATGTTTTTGATGCAGAGAAGCTGAGGAAGATAGGGTTTATTGTTTACTCTATTGGTAAGCCGTTGGACCAGTGGCACATGCCTGCTCTTGCTTAGCTCAGACTCTTTGCCCTTTCTCAAGATTTGGATTGTTTTTCTCTCTGTTGCTTATATCAAATAATTTGTTCTGTTTCTTCTTGACGAGATATTTTCCTATACTTATTATGTTGGTTAGAACAAGAGACTAGGTTTGGTTATTATTGCTAACT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + + + + + + + 5 + 119146348 + 26 + 71964315672 + 0.46 + 1.28 + 0.85 + + + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_chimera_vs_three_human_max1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,1 @@ +chimera ENA|AB011145|AB011145.1 100.00 4560 0 0 1 4560 121 4680 0.0 8421 diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_chimera_vs_three_human_max1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_chimera_vs_three_human_max1.txt Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,356 @@ +BLASTN 2.2.30+ + + +Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb +Miller (2000), "A greedy algorithm for aligning DNA sequences", J +Comput Biol 2000; 7(1-2):203-14. + + + +Database: Just 3 human mRNA sequences + 3 sequences; 10,732 total letters + + + +Query= chimera chunks of AB011145 plus M10051 plus BC112106 + +Length=9973 + Score E +Sequences producing significant alignments: (Bits) Value + + ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein,... 8421 0.0 + + +> ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, +partial cds. +Length=4796 + + Score = 8421 bits (4560), Expect = 0.0 + Identities = 4560/4560 (100%), Gaps = 0/4560 (0%) + Strand=Plus/Plus + +Query 1 GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC 60 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 121 GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC 180 + +Query 61 CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA 120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 181 CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA 240 + +Query 121 TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC 180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 241 TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC 300 + +Query 181 TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT 240 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 301 TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT 360 + +Query 241 TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA 300 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 361 TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA 420 + +Query 301 CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA 360 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 421 CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA 480 + +Query 361 TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA 420 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 481 TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA 540 + +Query 421 CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC 480 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 541 CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC 600 + +Query 481 TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA 540 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 601 TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA 660 + +Query 541 TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT 600 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 661 TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT 720 + +Query 601 TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG 660 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 721 TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG 780 + +Query 661 GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA 720 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 781 GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA 840 + +Query 721 TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA 780 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 841 TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA 900 + +Query 781 ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG 840 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 901 ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG 960 + +Query 841 TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA 900 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 961 TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA 1020 + +Query 901 CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC 960 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1021 CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC 1080 + +Query 961 AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT 1020 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1081 AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT 1140 + +Query 1021 CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA 1080 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1141 CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA 1200 + +Query 1081 ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC 1140 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1201 ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC 1260 + +Query 1141 CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA 1200 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1261 CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA 1320 + +Query 1201 TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG 1260 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1321 TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG 1380 + +Query 1261 CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC 1320 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1381 CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC 1440 + +Query 1321 TATGTGTatttttattttgaataaacagaaagaaattttgggtttttaatttttttCTCC 1380 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1441 TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC 1500 + +Query 1381 CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTaaaaaaaaaaaaaCCTGCTA 1440 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1501 CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA 1560 + +Query 1441 GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT 1500 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1561 GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT 1620 + +Query 1501 ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA 1560 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1621 ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA 1680 + +Query 1561 GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT 1620 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1681 GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT 1740 + +Query 1621 CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT 1680 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1741 CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT 1800 + +Query 1681 GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA 1740 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1801 GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA 1860 + +Query 1741 TTGCTTATGAAAATTCCATAGTGGTAtttttttGGATTCTTAATGTGTAACTTAAACATA 1800 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1861 TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA 1920 + +Query 1801 CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA 1860 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1921 CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA 1980 + +Query 1861 AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG 1920 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 1981 AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG 2040 + +Query 1921 GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG 1980 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2041 GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG 2100 + +Query 1981 AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT 2040 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2101 AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT 2160 + +Query 2041 TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT 2100 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2161 TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT 2220 + +Query 2101 TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACtt 2160 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2221 TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT 2280 + +Query 2161 tttttCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG 2220 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2281 TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG 2340 + +Query 2221 CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA 2280 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2341 CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA 2400 + +Query 2281 CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT 2340 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2401 CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT 2460 + +Query 2341 TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC 2400 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2461 TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC 2520 + +Query 2401 TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT 2460 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2521 TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT 2580 + +Query 2461 GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT 2520 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2581 GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT 2640 + +Query 2521 AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT 2580 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2641 AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT 2700 + +Query 2581 TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT 2640 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2701 TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT 2760 + +Query 2641 GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT 2700 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2761 GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT 2820 + +Query 2701 TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA 2760 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2821 TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA 2880 + +Query 2761 GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA 2820 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2881 GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA 2940 + +Query 2821 TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA 2880 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 2941 TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA 3000 + +Query 2881 TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT 2940 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3001 TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT 3060 + +Query 2941 AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT 3000 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3061 AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT 3120 + +Query 3001 TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT 3060 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3121 TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT 3180 + +Query 3061 ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT 3120 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3181 ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT 3240 + +Query 3121 GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA 3180 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3241 GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA 3300 + +Query 3181 GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT 3240 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3301 GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT 3360 + +Query 3241 GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT 3300 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3361 GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT 3420 + +Query 3301 TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT 3360 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3421 TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT 3480 + +Query 3361 TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT 3420 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3481 TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT 3540 + +Query 3421 AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG 3480 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3541 AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG 3600 + +Query 3481 AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC 3540 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3601 AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC 3660 + +Query 3541 TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT 3600 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3661 TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT 3720 + +Query 3601 CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA 3660 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3721 CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA 3780 + +Query 3661 GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT 3720 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3781 GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT 3840 + +Query 3721 TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT 3780 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3841 TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT 3900 + +Query 3781 GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT 3840 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3901 GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT 3960 + +Query 3841 TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG 3900 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 3961 TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG 4020 + +Query 3901 GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA 3960 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4021 GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA 4080 + +Query 3961 CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA 4020 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4081 CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA 4140 + +Query 4021 CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA 4080 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4141 CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA 4200 + +Query 4081 GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA 4140 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4201 GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA 4260 + +Query 4141 GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT 4200 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4261 GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT 4320 + +Query 4201 GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG 4260 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4321 GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG 4380 + +Query 4261 GAAACTTTTAGATGACATTCTACAAATTAtttttttCTTTAAATTAAAAGAACCTAGCCA 4320 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4381 GAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCA 4440 + +Query 4321 ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA 4380 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4441 ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA 4500 + +Query 4381 AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA 4440 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4501 AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA 4560 + +Query 4441 ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA 4500 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4561 ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA 4620 + +Query 4501 GGTTGTCAAGAAGGCttttttttttttcttttttAAACCTGAGGGCAAAAAGGAATGGAT 4560 + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Sbjct 4621 GGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGAT 4680 + + + +Lambda K H + 1.33 0.621 1.12 + +Gapped +Lambda K H + 1.28 0.460 0.850 + +Effective search space used: 106299490 + + + Database: Just 3 human mRNA sequences + Posted date: Dec 26, 2014 5:54 AM + Number of letters in database: 10,732 + Number of sequences in database: 3 + + + +Matrix: blastn matrix 1 -2 +Gap Penalties: Existence: 0, Extension: 2.5 diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_rhodopsin_vs_three_human.columns.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.columns.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,7 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 4301 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 4301 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 4301 1213 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 4301 1213 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 983 1213 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1047 1213 diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_rhodopsin_vs_three_human.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,7 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 83 0 1 1047 88 1134 0.0 1474 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 333 28 0 1 333 118 450 4e-132 460 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 243 19 2 3127 3368 782 1023 3e-93 331 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 173 10 0 1410 1582 448 620 3e-73 265 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 170 12 0 2854 3023 615 784 3e-68 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 959 81 0 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1048 129 2 1 1047 88 1134 0.0 1208 diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_rhodopsin_vs_three_human.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,549 @@ + + + + blastn + BLASTN 2.2.30+ + Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. + + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + 1e-40 + 1 + -2 + 0 + 0 + L;m; + + + + + 1 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 2 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 3 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 1474.75 + 798 + 0 + 1 + 1047 + 88 + 1134 + 1 + 1 + 964 + 964 + 0 + 1047 + ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCTCATCGTGCTTGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCACCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACCTGGGTCATGGCACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATGCGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGGCAGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCATGGTCATTGCTTTCCTGATCTGTTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGGTCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCTTCGCAAAGTCCTCCTCCATCTACAACCCTGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCCACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACCGGCCTAA + ATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAA + ||||| || || || ||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| | ||||||||||||| |||||||||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| || ||||||||||||||||| ||||||||||| |||||||| |||| || ||||||||||||||||| || ||| ||||||| || || || |||||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||| || ||||| |||||||| |||||||| ||||||||||| || |||||||||||||||||||||||||| |||||||| |||||||||||||| ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||||||||| |||| |||||||| || ||| | || |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||| ||||||| |||||||||||||||||||| || ||||| || | |||| |||||||||||||| ||||||||||| ||||||||| + + + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + + + 4 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 15 + 7453579 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 5 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 15 + 7453579 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 6 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 15 + 7453579 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 7 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + + + 0 + 0 + 16 + 20482300 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 8 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + + + 0 + 0 + 16 + 20482300 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 9 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 460.936 + 249 + 3.59583e-132 + 1 + 333 + 118 + 450 + 1 + 1 + 305 + 305 + 0 + 333 + GTGCCCTTCTCCAACAAGACAGGCGTGGTGCGCAGTCCCTTCGAGCATCCACAGTACTACCTGGCCGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTCGGCTTCCCCATCAACTTCCTCACGCTCTATGTCACGGTTCAGCACAAGAAGCTGCGTACGCCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCCGACCTCTTCATGGTCTTCGGAGGCTTCACCACCACCCTCTACACCTCCCTGCATGGATACTTTGTCTTCGGGCCTACGGGATGCAATCTGGAGGGCTTTTTTGCCACCCTGGGAGGT + GTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGT + |||||||||||||| ||| || ||||| ||||| ||||||||| | ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||| || ||||||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||| | || |||||||||| ||||||||||||||| |||||||||||||| ||||||||||| || ||||||||| |||||||||| |||||||||||||| ||| + + + 2 + 331.671 + 179 + 2.94161e-93 + 3127 + 3368 + 782 + 1023 + 1 + 1 + 222 + 222 + 2 + 243 + AGGCAGCTGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCCGAGAAGGAGGTCACCCGTATGGTCATCATCATGGTCATTGCTTTCCTAATCTGTTGGCTGCCGTATGCCGGCGTGGCATTCTACATCTTCACCCACCAGGGCTCTAACTTTGGCCCCATCTTCATGACCCTCCCGGCATTCTTTGCCAAG-TCGTCCTCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAG + AGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCG-CCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAG + |||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||| ||| |||| || ||| |||||||||||||||||||||||||||||||||| ||||| || ||||||||||||||| |||| || |||||||||||| || || ||||||||||||||||||||||||||||||||||||||||| + + + 3 + 265.191 + 143 + 3.02604e-73 + 1410 + 1582 + 448 + 620 + 1 + 1 + 163 + 163 + 0 + 173 + GGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTATGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCCTTGCCCTCACCTGGGTCATGGCACTGGCCTGCGCCGCGCCCCCGCTAGTCGGCTGGTCCAGGTA + GGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||| ||||| |||||||||||||||| |||||||||||||| ||||| || | ||||||||||||||| + + + 4 + 248.571 + 134 + 3.04752e-68 + 2854 + 3023 + 615 + 784 + 1 + 1 + 158 + 158 + 0 + 170 + CAGGTACATCCCAGAGGGCATGCAGTGCTCATGTGGAATCGACTACTACACCCTCAAGCCGGAGGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCTATGATTGTCATATTCTTTTGCTATGGACAGCTGGTCTTCACCGTCAAGGAGG + CAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGG + |||||||||||| |||||| |||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| |||||| |||| || || |||||||| ||||| ||||||||||||||||||| + + + + + + + 0 + 0 + 16 + 20482300 + 0.46 + 1.28 + 0.85 + + + + + 10 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + + + 0 + 0 + 15 + 4628008 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 11 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + + + 0 + 0 + 15 + 4628008 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 12 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 1323.32 + 716 + 0 + 1 + 959 + 118 + 1076 + 1 + 1 + 878 + 878 + 0 + 959 + GTGCCCTTCTCCAACAAGACGGGTGTGGTGCGCAGCCCCTTCGAGTACCCGCAGTACTACCTGGCTGAGCCCTGGCAGTTCTCCATGCTGGCTGCCTACATGTTTCTGCTGATCGTGCTCGGATTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCTGTGGCCAACCTCTTCATGGTCTTTGGAGGCTTCACCACCACCCTGTATACCTCTATGCATGGATACTTCGTCTTCGGGGCCACGGGATGCAATCTGGAGGGCTTCTTTGCCACGCTGGGCGGTGAAATCGCCCTGTGGTCCCTGGTGGTCCTGGCCATCGAGCGGTATGTGGTGGTCTGCAAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCACGCCATCATGGGCCTCGCCTTCACGTGGGTCATGGCACTGGCCTGCGCTGCACCCCCACTAGCCGGCTGGTCCAGGTACATCCCAGAGGGCATGCAGTGCTCGTGTGGGATTGACTACTACACGCTCAAACCGGAGGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTGTCATTTTCTTCTGCTACGGACAGCTGGTGTTCACAGTGAAGGAGGCGGCTGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCCGAGAAGGAAGTCACGCGCATGGTCATCATCATGGTCGTTGCGTTCCTAATCTGTTGGCTGCCCTACGCCAGCGTGGCATTCTACATCTTTACCCACCAGGGCTCTAACTTTGGCCCTGTCTTCATGACCATCCCGGCATTCTTCGCCAAGTCATCCTCCATCTACAACCCGGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCCTCTGCTGTGGCAAGAACCCACTGGGTGA + GTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGA + |||||||||||||| |||||||||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| |||||||||||||| | || |||||||||| |||||| || |||||| ||||||||||||||||||||||| |||| ||||||||| ||||||||||||||||||| |||||||||||||| |||||||||||| ||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||| ||||||||||| |||||||||||| | |||||||| ||||||||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| |||||| |||||||||||||||| || ||||||||||||||||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||| |||| || |||||||| || ||||| || ||||| || |||||||| ||||||||||||||||||||||||||||| |||||||| |||||||| ||||| ||||||||||||||||||||| | || ||||| ||||| ||| ||||||||||||||||||||||||||||||| |||||||||||||| ||||| || || |||||||||||||||| || ||||| |||||| || ||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||||||||||||||||| + + + + + + + 0 + 0 + 15 + 4628008 + 0.46 + 1.28 + 0.85 + + + + + 13 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 14 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 15 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + 1 + Subject_3 + ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds + Subject_3 + 1213 + + + 1 + 1208.83 + 654 + 0 + 1 + 1047 + 88 + 1134 + 1 + 1 + 917 + 917 + 2 + 1048 + ATGAACGGGACCGAGGGCCCAAACTTCTACGTGCCTTTCTCCAACAAGACGGGCGTCGTACGCAGCCCCTTCGAGGCGCCGCAGTACTACCTGGCTGAGCCATGGCAGTTCAGCATGCTGGCCGCCTACATGTTCCTGCTGATCATGCTTGGCTTCCCCATCAACTTCCTCACGCTGTACGTCACAGTCCAGCACAAGAAGCTGAGGACCCCCCTCAACTACATCCTGCTCAACCTGGCCGTGGCAGATCTCTTCATGGTGTTCGGGGGCTTCACCACCACCCTGTATACCTCTCTGCACGGGTACTTCGTGTTCGGTCCGACGGGCTGCAACCTCGAGGGCTTCTTTGCCACCTTAGGCGGTGAAATTGCACTGTGGTCCTTGGTGGTGCTAGCCATCGAGCGGTACGTAGTGGTGTGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCGTCGCATTCACCTGGGTCATGGCTCTGGCCTGTGCGGCCCCCCCCCTCGTCGGCTGGTCTAGATACATCCCGGAGGGGATGCAGTGCTCGTGCGGGATCGATTACTACACGCCCCACGAGGAGACCAACAATGAGTCGTTCGTCATCTACATGTTCGTTGTACACTTCATCATCCCCCTGATTGTCATATTCTTCTGCTACGGGCAGCTGGTCTTCACCGTCAAGGAGGCTGCAGCCCAGCAGCAGGAGTCGGCCACCACTCAGAAGGCCGAGAAGGAGGTCACGCGTATGGTCATCATCATGGTCATCGCTTTCCTCATATGCTGGCTGCCCTACGCAGGTGTGGCGTTCTACATCTTCACCCATCAGGGATCCGACTTTGGCCCCATCTTCATGACCATCCCGGCTTTCTTTGCCAAGA-CGTCTGCCGTCTATAACCCCGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGGTCACCACTCTCTGCTGTGGCAAGAACCCCCTAGGTGACGACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCCTGCCTAA + ATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCC-GCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAA + ||||| || || || ||||| |||||||||||||| |||||||| |||||| || |||||||||||||||||| || |||||||||||||||||||||||||||||| ||||||||||||||||||||| ||||||||| |||| |||||||||||||||||||||||||| |||||||| |||||||||||||||||| | || || ||||||||||||||||||||||| |||||||| || ||||||||||| | || |||||||||| |||||| || ||||||||||| || |||||||| ||||| || || || ||||| | |||||||||||||||||| | |||||||||||||| ||||||||||||||||| || ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||| |||||||| || || ||||| |||| ||||||||| || |||||||| ||||| ||||||||||||| || ||||| |||||||||| | | |||| |||||| ||||| || ||||||||||||||||| || ||||||| ||||||| ||||| |||| || |||||||| |||||||| |||||||||||||||||||| || ||||||||||||||||| |||||||| |||||||| |||||||||||||| || ||||||||||||||||||||||||||||| || |||||| |||||||||| | ||||| ||||||||||||||||| ||||| ||| |||| || |||||||||||||||||||| || ||||||||||||| || | ||| |||| ||||| |||||||| ||||||||||||||||||||||||||||||||| ||||||| ||||||| ||||||||||| || |||||||| |||||||| | |||||||||||||| ||||| ||||| |||||||| |||||| + + + + + + + 0 + 0 + 15 + 4933992 + 0.46 + 1.28 + 0.85 + + + + + 16 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 15 + 6353949 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 17 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 15 + 6353949 + 0.46 + 1.28 + 0.85 + + + No hits found + + + 18 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 15 + 6353949 + 0.46 + 1.28 + 0.85 + + + No hits found + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/blastn_rhodopsin_vs_three_human_converted.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human_converted.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,7 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 83 0 1 1047 88 1134 0.0 1474 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 333 28 0 1 333 118 450 4e-132 460 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 243 19 2 3127 3368 782 1023 3e-93 331 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 173 10 0 1410 1582 448 620 3e-73 265 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 170 12 0 2854 3023 615 784 3e-68 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 959 81 0 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1048 129 2 1 1047 88 1134 0.0 1208 diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_four_human_vs_rhodopsin.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,6 @@ +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_four_human_vs_rhodopsin.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,665 @@ + + + + blastp + BLASTP 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + BLOSUM62 + 1e-08 + 11 + 1 + F + + + + + 1 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 5 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + sp|Q9BS26|ERP44_HUMAN + Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 30 + 119568 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 9 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + sp|Q9NSY1|BMP2K_HUMAN + BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 38 + 348130 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 13 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 17 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + sp|P06213|INSR_HUMAN + Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 39 + 414987 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|57163783|ref|NP_001009242.1| + rhodopsin [Felis catus] + NP_001009242 + 348 + + + 1 + 701.049 + 1808 + 0 + 1 + 348 + 1 + 348 + 0 + 0 + 336 + 343 + 0 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 20 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|3024260|sp|P56514.1|OPSD_BUFBU + RecName: Full=Rhodopsin + P56514 + 354 + + + 1 + 619.002 + 1595 + 0 + 1 + 341 + 1 + 342 + 0 + 0 + 290 + 322 + 1 + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE + MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE + MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 21 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|283855846|gb|ADB45242.1| + rhodopsin [Cynopterus brachyotis] + ADB45242 + 328 + + + 1 + 653.284 + 1684 + 0 + 11 + 338 + 1 + 328 + 0 + 0 + 311 + 321 + 0 + 328 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS + VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 22 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|283855823|gb|ADB45229.1| + rhodopsin [Myotis pilosus] + ADB45229 + 328 + + + 1 + 631.328 + 1627 + 0 + 11 + 338 + 1 + 328 + 0 + 0 + 311 + 323 + 0 + 328 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS + VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T S + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 23 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|223523|prf||0811197A + rhodopsin [Bos taurus] + 0811197A + 347 + + + 1 + 673.315 + 1736 + 0 + 1 + 348 + 1 + 347 + 0 + 0 + 324 + 336 + 1 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + 24 + sp|P08100|OPSD_HUMAN + Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|12583665|dbj|BAB21486.1| + fresh water form rod opsin [Conger myriaster] + BAB21486 + 354 + + + 1 + 599.356 + 1544 + 0 + 1 + 341 + 1 + 342 + 0 + 0 + 281 + 314 + 1 + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE + MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE + MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +D ASAT SKTE + + + + + + + 0 + 0 + 29 + 101761 + 0.041 + 0.267 + 0.14 + + + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_four_human_vs_rhodopsin_converted.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,6 @@ +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,6 @@ +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 rhodopsin [Felis catus] +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 RecName: Full=Rhodopsin +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 rhodopsin [Cynopterus brachyotis] +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 rhodopsin [Myotis pilosus] +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 rhodopsin [Bos taurus] +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 fresh water form rod opsin [Conger myriaster] diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_four_human_vs_rhodopsin_ext.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,6 @@ +sp|P08100|OPSD_HUMAN gi|57163783|ref|NP_001009242.1| 96.55 348 12 0 1 348 1 348 0.0 701 gi|57163783|ref|NP_001009242.1| 1808 336 343 0 98.56 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 348 N/A +sp|P08100|OPSD_HUMAN gi|3024260|sp|P56514.1|OPSD_BUFBU 84.80 342 51 1 1 341 1 342 0.0 619 gi|3024260|sp|P56514.1|OPSD_BUFBU 1595 290 322 1 94.15 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 354 N/A +sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A +sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 N/A +sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 N/A +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 N/A diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_human_vs_pdb_seg_no.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_human_vs_pdb_seg_no.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,322 @@ + + + + blastp + BLASTP 2.2.24+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /data/blastdb/pdbaa + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + BLOSUM62 + 1e-08 + 11 + 1 + F + + + + + 1 + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + 1 + gi|193885198|pdb|2R2J|A + Chain A, Crystal Structure Of Human Erp44 + 2R2J_A + 382 + + + 1 + 768.073791748238 + 1982 + 0 + 26 + 406 + 2 + 382 + 0 + 0 + 370 + 372 + 0 + 381 + PVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL + PLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL + P+ +EITSLDTENIDEILNNADVALVNFYADWCRFSQ LHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNG KREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPD VYLGA TNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFH KEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRH YVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL + + + + + 2 + gi|88192228|pdb|2B5E|A + Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase >gi|206581884|pdb|3BOA|A Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase. + 2B5E_A + 504 + + + 1 + 95.130132620622 + 235 + 4.15033135540548e-20 + 25 + 306 + 10 + 283 + 0 + 0 + 73 + 133 + 24 + 290 + TPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH + APEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH + P + + L T++ +E + + D+ L F+A WC + + P + +A++ + E+ + A++DC ++ D+ + I +P+LK+F+N + +Y G R+ +A+ ++ +Q + + DL + +I + D+D F +AN +D F+SA + D+ IY P P +VY G + + DV W+Q + +P EI + E GLP LF+ D E LE ++ +G +NF+ D KF RH + + + + + + + 49615 + 11554246 + 0 + 2039204827 + 0.041 + 0.267 + 0.14 + + + + + 2 + Query_2 + sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + 1 + gi|73536291|pdb|2BUJ|A + Chain A, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine >gi|73536292|pdb|2BUJ|B Chain B, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine + 2BUJ_A + 317 + + + 1 + 105.530521170391 + 262 + 1.04156432658542e-22 + 40 + 308 + 21 + 294 + 0 + 0 + 82 + 130 + 15 + 279 + GVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI + GHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI + G V +H + +++ L EGGFS V LV H G ALKR+ + D +RE M L H NI+ + + E +L+ + + G + N++ + G TE ++L + C + +H HRDLK NILL D G VL D GS ++ + +++ + T+SYRAPE+ ++ I + D+W+LGC+LY + F P+ G+S +IP + R+S + L+ M+ DP RP I + + + + + 2 + gi|270346335|pdb|2WQM|A + Chain A, Structure Of Apo Human Nek7 >gi|270346336|pdb|2WQN|A Chain A, Structure Of Adp-Bound Human Nek7 + 2WQM_A + 310 + + + 1 + 86.2705423745229 + 212 + 6.48475818195287e-17 + 53 + 311 + 36 + 288 + 0 + 0 + 74 + 129 + 32 + 272 + LEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV + IEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV + +E+ + G FS V+ G+ ALK++ + ++ D C +EI ++K+L+ H N++ Y + I DN E+ I++E AG + + KK + E V + F C A+ +H + ++HRD+K N+ + G L D G +F + + + + T Y +PE I+ G K+DIW+LGCLLY++ PF ++ ++C ++ + YS + L+ + PDPE RPD+ V + + + + + + + 49615 + 11554246 + 0 + 6524204778 + 0.041 + 0.267 + 0.14 + + + + + 3 + Query_3 + sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + 1 + gi|116667097|pdb|2DTG|E + Chain E, Insulin Receptor (Ir) Ectodomain In Complex With Fab's + 2DTG_E + 897 + + + 1 + 1846.24740474091 + 4781 + 0 + 28 + 955 + 1 + 897 + 0 + 0 + 890 + 893 + 31 + 928 + HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA + HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV------------PRPSRKRRSLGDVGNA-------------------GNNEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA + HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDN+IVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV PRPSRKRRSLGDVGN + EEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLC +RKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA + + + + + 2 + gi|114794482|pdb|2HR7|A + Chain A, Insulin Receptor (Domains 1-3) >gi|114794483|pdb|2HR7|B Chain B, Insulin Receptor (Domains 1-3) + 2HR7_A + 486 + + + 1 + 1016.91271779085 + 2628 + 0 + 28 + 512 + 1 + 485 + 0 + 0 + 483 + 485 + 0 + 485 + HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKI + HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDKASCENELLKFSYIRTSFDKI + HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDN+IVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGD+ASCENELLKFSYIRTSFDKI + + + + + + + 49615 + 11554246 + 0 + 7824126603 + 0.041 + 0.267 + 0.14 + + + + + 4 + Query_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + gi|16975387|pdb|1JFP|A + Chain A, Structure Of Bovine Rhodopsin (Dark Adapted) >gi|22219255|pdb|1LN6|A Chain A, Structure Of Bovine Rhodopsin (Metarhodopsin Ii) >gi|157878065|pdb|1GZM|A Chain A, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form >gi|157878066|pdb|1GZM|B Chain B, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form >gi|157878298|pdb|1HZX|A Chain A, Crystal Structure Of Bovine Rhodopsin >gi|157878299|pdb|1HZX|B Chain B, Crystal Structure Of Bovine Rhodopsin >gi|157878979|pdb|1L9H|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution >gi|157878980|pdb|1L9H|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution >gi|157880263|pdb|1U19|A Chain A, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution >gi|157880264|pdb|1U19|B Chain B, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution >gi|157883606|pdb|2G87|A Chain A, Crystallographic Model Of Bathorhodopsin >gi|157883607|pdb|2G87|B Chain B, Crystallographic Model Of Bathorhodopsin >gi|157883830|pdb|2HPY|A Chain A, Crystallographic Model Of Lumirhodopsin >gi|157883831|pdb|2HPY|B Chain B, Crystallographic Model Of Lumirhodopsin >gi|157883860|pdb|2I35|A Chain A, Crystal Structure Of Rhombohedral Crystal Form Of Ground- State Rhodopsin >gi|157883861|pdb|2I36|A Chain A, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin >gi|157883862|pdb|2I36|B Chain B, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin >gi|157883863|pdb|2I36|C Chain C, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin >gi|157883864|pdb|2I37|A Chain A, Crystal Structure Of A Photoactivated Rhodopsin >gi|157883865|pdb|2I37|B Chain B, Crystal Structure Of A Photoactivated Rhodopsin >gi|157883866|pdb|2I37|C Chain C, Crystal Structure Of A Photoactivated Rhodopsin >gi|159795066|pdb|2PED|A Chain A, Crystallographic Model Of 9-Cis-Rhodopsin >gi|159795067|pdb|2PED|B Chain B, Crystallographic Model Of 9-Cis-Rhodopsin >gi|192988480|pdb|3CAP|A Chain A, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State >gi|192988481|pdb|3CAP|B Chain B, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State >gi|195927457|pdb|3C9L|A Chain A, Structure Of Ground-State Bovine Rhodospin In A Hexagonal Crystal Form >gi|197107530|pdb|1F88|A Chain A, Crystal Structure Of Bovine Rhodopsin >gi|197107531|pdb|1F88|B Chain B, Crystal Structure Of Bovine Rhodopsin >gi|206582030|pdb|3DQB|A Chain A, Crystal Structure Of The Active G-Protein-Coupled Receptor Opsin In Complex With A C-Terminal Peptide Derived From The Galpha Subunit Of Transducin + 1JFP_A + 348 + + + 1 + 681.018687590916 + 1756 + 0 + 1 + 348 + 1 + 348 + 0 + 0 + 325 + 337 + 0 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA + + + + + 2 + gi|195927458|pdb|3C9M|A + Chain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal Crystal Form + 3C9M_A + 348 + + + 1 + 674.085095224404 + 1738 + 0 + 1 + 348 + 1 + 348 + 0 + 0 + 324 + 335 + 0 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + M GTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA + + + + + + + 49615 + 11554246 + 0 + 1672994000 + 0.041 + 0.267 + 0.14 + + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_human_vs_pdb_seg_no_converted_ext.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,8 @@ +sp|Q9BS26|ERP44_HUMAN gi|193885198|pdb|2R2J|A 97.11 381 11 0 26 406 2 382 0.0 768 gi|193885198|pdb|2R2J|A 1982 370 372 0 97.64 1 1 PVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL PLGSEITSLDTENIDEILNNADVALVNFYADWCRFSQXLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGXXXKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDXVYLGAXTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHXKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPVIAIDSFRHXYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL 406 382 Chain A, Crystal Structure Of Human Erp44 +sp|Q9BS26|ERP44_HUMAN gi|88192228|pdb|2B5E|A 25.17 290 193 8 25 306 10 283 4e-20 95.1 gi|88192228|pdb|2B5E|A;gi|206581884|pdb|3BOA|A 235 73 133 24 45.86 1 1 TPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKR-EYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNI---IYKPPGHSAPDMVYLGA---MTNFDVTYNWIQDKCVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKF-RH APEDSAVVKLATDSFNEYIQSHDLVLAEFFAPWCGHCKNMAPEYVKAAETLVEK-----NITLAQIDCTENQDLCMEHNIPGFPSLKIFKNSDVNNSIDYEGPRTAEAIVQFMIKQSQPAVAVVADLPAYLANETFVTPVIVQSGKIDADFNATFYSMANKHFNDYDFVSA--------ENADDDFKLSIYLPSAMDEP-VVYNGKKADIADADVFEKWLQVEALPYFGEIDGSVFAQYVESGLPLGYLFY--NDEEELEEYKPLFTELAKKNRGLMNFVSIDARKFGRH 406 504 Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase<>Chain A, Crystal Structure Of Yeast Protein Disulfide Isomerase. +sp|Q9NSY1|BMP2K_HUMAN gi|73536291|pdb|2BUJ|A 29.39 279 182 8 40 308 21 294 1e-22 105 gi|73536291|pdb|2BUJ|A;gi|73536292|pdb|2BUJ|B 262 82 130 15 46.59 1 1 GVRVFAVGRHQVTLEESLAEGGFSTVFLVR-THGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTG--FTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDG-VNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPF------GESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDI GHMVIIDNKHYLFIQK-LGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREEAQREAD-MHRLFNHPNILRLVAYCLRERGAKH-EAWLLLPFFKRGTLWNEIERLKDKGNFLTEDQILWLLLGICRGLEAIH--AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALTLQDWAAQRCTISYRAPELFSVQSHCVIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLSIPQSPRHSSALWQLLNSMMTVDPHQRPHI 1161 317 Chain A, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine<>Chain B, Crystal Structure Of The Human Serine-Threonine Kinase 16 In Complex With Staurosporine +sp|Q9NSY1|BMP2K_HUMAN gi|270346335|pdb|2WQM|A 27.21 272 166 12 53 311 36 288 6e-17 86.3 gi|270346335|pdb|2WQM|A;gi|270346336|pdb|2WQN|A 212 74 129 32 47.43 1 1 LEESLAEGGFSTVFLVRTH-GGIRCALKRMYVNNMPDLNV---CKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMN--KKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGGKPITTKADIWALGCLLYKLCFFTLPFGESQV---AICD----GNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQV IEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLN-HPNVIKYY---ASFIEDN--ELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRR--VMHRDIKPANVFITATGVVKLGDLG--LGRFFSSKTTAAHSL------VGTPYYMSPERIHENG---YNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYV 1161 310 Chain A, Structure Of Apo Human Nek7<>Chain A, Structure Of Adp-Bound Human Nek7 +sp|P06213|INSR_HUMAN gi|116667097|pdb|2DTG|E 95.91 928 7 2 28 955 1 897 0.0 1846 gi|116667097|pdb|2DTG|E 4781 890 893 31 96.23 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQILKELEESSFRKTFEDYLHNVVFV------------PRPSRKRRSLGDVGNA-------------------GNNEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCDTRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIA 1382 897 Chain E, Insulin Receptor (Ir) Ectodomain In Complex With Fab's +sp|P06213|INSR_HUMAN gi|114794482|pdb|2HR7|A 99.59 485 2 0 28 512 1 485 0.0 1016 gi|114794482|pdb|2HR7|A;gi|114794483|pdb|2HR7|B 2628 483 485 0 100.00 1 1 HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDQASCENELLKFSYIRTSFDKI HLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNHIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECLGNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRSYALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQERNDIALKTNGDKASCENELLKFSYIRTSFDKI 1382 486 Chain A, Insulin Receptor (Domains 1-3)<>Chain B, Insulin Receptor (Domains 1-3) +sp|P08100|OPSD_HUMAN gi|16975387|pdb|1JFP|A 93.39 348 23 0 1 348 1 348 0.0 681 gi|16975387|pdb|1JFP|A;gi|22219255|pdb|1LN6|A;gi|157878065|pdb|1GZM|A;gi|157878066|pdb|1GZM|B;gi|157878298|pdb|1HZX|A;gi|157878299|pdb|1HZX|B;gi|157878979|pdb|1L9H|A;gi|157878980|pdb|1L9H|B;gi|157880263|pdb|1U19|A;gi|157880264|pdb|1U19|B;gi|157883606|pdb|2G87|A;gi|157883607|pdb|2G87|B;gi|157883830|pdb|2HPY|A;gi|157883831|pdb|2HPY|B;gi|157883860|pdb|2I35|A;gi|157883861|pdb|2I36|A;gi|157883862|pdb|2I36|B;gi|157883863|pdb|2I36|C;gi|157883864|pdb|2I37|A;gi|157883865|pdb|2I37|B;gi|157883866|pdb|2I37|C;gi|159795066|pdb|2PED|A;gi|159795067|pdb|2PED|B;gi|192988480|pdb|3CAP|A;gi|192988481|pdb|3CAP|B;gi|195927457|pdb|3C9L|A;gi|197107530|pdb|1F88|A;gi|197107531|pdb|1F88|B;gi|206582030|pdb|3DQB|A 1756 325 337 0 96.84 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 348 Chain A, Structure Of Bovine Rhodopsin (Dark Adapted)<>Chain A, Structure Of Bovine Rhodopsin (Metarhodopsin Ii)<>Chain A, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form<>Chain B, Structure Of Bovine Rhodopsin In A Trigonal Crystal Form<>Chain A, Crystal Structure Of Bovine Rhodopsin<>Chain B, Crystal Structure Of Bovine Rhodopsin<>Chain A, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution<>Chain B, Crystal Structure Of Bovine Rhodopsin At 2.6 Angstroms Resolution<>Chain A, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution<>Chain B, Crystal Structure Of Bovine Rhodopsin At 2.2 Angstroms Resolution<>Chain A, Crystallographic Model Of Bathorhodopsin<>Chain B, Crystallographic Model Of Bathorhodopsin<>Chain A, Crystallographic Model Of Lumirhodopsin<>Chain B, Crystallographic Model Of Lumirhodopsin<>Chain A, Crystal Structure Of Rhombohedral Crystal Form Of Ground- State Rhodopsin<>Chain A, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain B, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain C, Crystal Structure Of Trigonal Crystal Form Of Ground-State Rhodopsin<>Chain A, Crystal Structure Of A Photoactivated Rhodopsin<>Chain B, Crystal Structure Of A Photoactivated Rhodopsin<>Chain C, Crystal Structure Of A Photoactivated Rhodopsin<>Chain A, Crystallographic Model Of 9-Cis-Rhodopsin<>Chain B, Crystallographic Model Of 9-Cis-Rhodopsin<>Chain A, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State<>Chain B, Crystal Structure Of Native Opsin: The G Protein-Coupled Receptor Rhodopsin In Its Ligand-Free State<>Chain A, Structure Of Ground-State Bovine Rhodospin In A Hexagonal Crystal Form<>Chain A, Crystal Structure Of Bovine Rhodopsin<>Chain B, Crystal Structure Of Bovine Rhodopsin<>Chain A, Crystal Structure Of The Active G-Protein-Coupled Receptor Opsin In Complex With A C-Terminal Peptide Derived From The Galpha Subunit Of Transducin +sp|P08100|OPSD_HUMAN gi|195927458|pdb|3C9M|A 93.10 348 24 0 1 348 1 348 0.0 674 gi|195927458|pdb|3C9M|A 1738 324 335 0 96.26 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 348 Chain A, Structure Of A Mutant Bovine Rhodopsin In Hexagonal Crystal Form diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_human_vs_pdb_seg_no_converted_std.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,8 @@ +sp|Q9BS26|ERP44_HUMAN gi|193885198|pdb|2R2J|A 97.11 381 11 0 26 406 2 382 0.0 768 +sp|Q9BS26|ERP44_HUMAN gi|88192228|pdb|2B5E|A 25.17 290 193 8 25 306 10 283 4e-20 95.1 +sp|Q9NSY1|BMP2K_HUMAN gi|73536291|pdb|2BUJ|A 29.39 279 182 8 40 308 21 294 1e-22 105 +sp|Q9NSY1|BMP2K_HUMAN gi|270346335|pdb|2WQM|A 27.21 272 166 12 53 311 36 288 6e-17 86.3 +sp|P06213|INSR_HUMAN gi|116667097|pdb|2DTG|E 95.91 928 7 2 28 955 1 897 0.0 1846 +sp|P06213|INSR_HUMAN gi|114794482|pdb|2HR7|A 99.59 485 2 0 28 512 1 485 0.0 1016 +sp|P08100|OPSD_HUMAN gi|16975387|pdb|1JFP|A 93.39 348 23 0 1 348 1 348 0.0 681 +sp|P08100|OPSD_HUMAN gi|195927458|pdb|3C9M|A 93.10 348 24 0 1 348 1 348 0.0 674 diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_rhodopsin_vs_four_human.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_rhodopsin_vs_four_human.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,6 @@ +gi|57163783|ref|NP_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 348 1 348 0.0 701 +gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 0.0 605 +gi|283855846|gb|ADB45242.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630 +gi|283855823|gb|ADB45229.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630 +gi|223523|prf||0811197A sp|P08100|OPSD_HUMAN 93.10 348 23 1 1 347 1 348 0.0 651 +gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 0.0 587 diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_sample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_sample.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,293 @@ + + + + blastp + BLASTP 2.2.24+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + nr + Query_1 + Sample + 516 + + + BLOSUM62 + 1e-30 + 11 + 1 + F + + + + + 1 + Query_1 + Sample + 516 + + + 1 + gi|119953746|ref|YP_950551.1| + tail tape measure protein [Streptococcus phage SMP] >gi|118430558|gb|ABK91882.1| tail tape measure protein [Streptococcus suis phage SMP] + YP_950551 + 659 + + + 1 + 949.117592429394 + 2452 + 0 + 1 + 516 + 27 + 542 + 0 + 0 + 500 + 500 + 0 + 516 + FHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + FHLLNSGGSALSVMFAKLVGIIAGISAPIWAVIGVIAALVAGFVLLYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + FHLLNSGGSALSVMFAKLVGIIAGISAPIW YNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + + + + + 2 + gi|148986157|ref|ZP_01819143.1| + unknown phage protein [Streptococcus pneumoniae SP3-BS71] >gi|147921871|gb|EDK72998.1| unknown phage protein [Streptococcus pneumoniae SP3-BS71] + ZP_01819143 + 1031 + + + 1 + 174.481245259597 + 441 + 1.54640812741294e-41 + 49 + 300 + 679 + 897 + 0 + 0 + 104 + 148 + 33 + 252 + TNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS + TNEGFRDAVTTVWNAILEVINAVVSEISNFVMSIFGTVVTWWTENQELIRTSAETVWNAIYTVISTILDILGPLLQAGWDNIQLIITTTWEIIKIVVETAINVVLGVIQAVMQIITGDWSGAWETIKGVFSTVWQAIQSIVQT-------IFSAIQSYISNILNGISGT----VSNIWNSIKDTVSN----------------------VLNAISSTVSSVWEGIKSTISSAINGARDAVSSAIEAIKGLFN + TNE FR V W AI I+ V + +FVM ++G +V WW ENQELIR +AETVWNAI TV+ T++ L P++Q WD I ++TT +IK VV+T + VVLG+I+AVMQ+I GDWSGAWET+KGV T+W+ I+S+VQ IF +++ +I + + GT V IW+ IK TVSN V NAIS+ S++W I +T+ S + + + +E IK +++ + + + + + 3 + gi|77411259|ref|ZP_00787609.1| + tail tape meausure protein [Streptococcus agalactiae CJB111] >gi|77162685|gb|EAO73646.1| tail tape meausure protein [Streptococcus agalactiae CJB111] + ZP_00787609 + 1039 + + + 1 + 165.621655013498 + 418 + 7.61538823982138e-39 + 50 + 310 + 655 + 904 + 0 + 0 + 107 + 158 + 11 + 261 + NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVF + HEGFRTAVTEIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQ-------FISNSWNGIKGTMTNLL----NSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTITNAINGAKNAVSSAINAIKNLF + +E FRT V W AI + +S ++ + SFVM +WG + WW ENQ+LI A TVW AI TV++T+MT L P +Q +W+ I ++TT ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V T+WE IKSL+ + + + Q F+ + W+ + GT+ ++ + IK+ VSN ++ I +I++SI +T +VWN + S + + IS TV SV + I + K S+A IK +F + + + + + 4 + gi|76786754|ref|YP_329383.1| + prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909] >gi|76561811|gb|ABA44395.1| prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909] + YP_329383 + 1039 + + + 1 + 159.073262222903 + 401 + 6.55719737745379e-37 + 50 + 310 + 655 + 904 + 0 + 0 + 103 + 156 + 11 + 261 + NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVF + HEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQ-------FISNSWNGIKGTMTNLL----NSIKGVVSNVWNGIKSTISSILSSIGSTVSSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNAINGAKNAVSSAINAIKNLF + +E FRT V W AI + ++ ++ + SFVM +WG ++ WW ENQ+LI TVW AI TV++T+MT L P +Q +W+ I ++TT ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V T+WE IKSL+ + + + Q F+ + W+ + GT+ ++ + IK VSN + I +I++SI +T ++WN + S + + IS+TV V + I + K S+A IK +F + + + + + 5 + gi|153811333|ref|ZP_01964001.1| + hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174] >gi|149832460|gb|EDM87544.1| hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174] + ZP_01964001 + 1228 + + + 1 + 157.147264343316 + 396 + 2.33083876931167e-36 + 3 + 516 + 573 + 1059 + 0 + 0 + 167 + 247 + 113 + 557 + LLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQV---AIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLI-----------KQAISNAWEIIKTKT-----------------------SEIWNAITTFLSGIWEGIKTAASTAWEWIKTT-ISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIEN-IKSTVSNGWNNL---VSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLI-NGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + LVKAGG--FSGVFTKALGLI---TSPAAIVVGVIAAITAVIIHLWNTNEDFRNTITAIWQKIKDAFTT---------------FAAGISERLSALGITFSDVTSAIKTIWDGFCNLLAPVLEAAFSTIAIALQTAFNVI-----------LGIWDVFSAVFSGDWSGAWEAIKGIFSSIWDGLKEYFSTIIGAVKGVADVF---LGWFGTNWETVWNGVKTFFEGIW--------NGISSFFEGI--------------WNGISTFCTTVWNGIVTNVTAFCTTVHDTISTIFNAVKDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNA---IKTTVQTVF-NAVKTTVTTIWNAIKTGTSTAWN----AVKTAVTTPINAAKSAVTSAIN------GIKS + L+ +GG S +F K +G+I ++P +NTNE+FR + A W+ IK A +T A +E + T V +AI+T+ + L P+++ A+ I + T NVI LGI + +GDWSGAWE +KG+ +IW+G+K A+ G+ +F L + + W+TVW + IW N I++ +E I WN IST + +W I T V + TT+ I T +K V S WE IK V ++ IV +V F+LI + I + WE IK+ + +WNAI T + + IK+A TAW ++K ++ VM I + I T WN IKT+ + +N IKSA + AWN +K+++ T + N IK+ ++ WN + V TV NA I + V+T F NAV I NAI G N VK A I+A AV+ AI+ GIKS + + + + + 6 + gi|56962696|ref|YP_174422.1| + hypothetical protein ABC0922 [Bacillus clausii KSM-K16] >gi|56908934|dbj|BAD63461.1| phage-related protein [Bacillus clausii KSM-K16] + YP_174422 + 593 + + + 1 + 146.746875793547 + 369 + 3.12404663750498e-33 + 48 + 433 + 123 + 465 + 0 + 0 + 112 + 187 + 49 + 389 + NTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGL---VQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSN + QTNETFRNGVIQAWEAIKTTMETVVATIVTFVSEKLAQIKAFWDEHGAAVMQAVTNIFNGIKSIIEPVMNGILAIMQFVWPFIVSLIQMVWGNIQGVISGALNIIMGLVKAFAGLFTGDFS-----------LMWEGIKQLFSGALEAIWNVVQLLLFGR--LLKIASSLFTGLMGVFSKMWGAISNLFLTALNGIRSFFSTIFTPIQ-------NVVMTVMGFIRNAISTG----LTTASNVVQTVLTAIRTVFLTVFNAVRNV-----------VTTAISFVQNFISTGISAARTAVTSALNAIKTTFTTIFNAVRSSVTTAMTNIKTAISN-------GIQSAWQ----AVLNFVGRFREAGKNIVNSIAEGITSAIGAVKNAISN + TNE FR V AWEAIK+ + T V +V+FV + Q+ A+W+E+ + Q ++N I++++E VM ++ I+Q W I++++ V I+ V+ L +++G++KA + GD+S +WEGIK L A++ + VQ+ G L I +++ +M V +W I A+ + I T IQ N + TV I AIST LTT +QT L I+TV+ + ++ V VT ++ IS +T + NAI T + I+ ++++ +TA IKT ISN I++AW ++ N + + A +N N+I I++AI +K+ +SN + + + + + 7 + gi|50914476|ref|YP_060448.1| + unknown phage protein [Streptococcus pyogenes MGAS10394] >gi|40218580|gb|AAR83234.1| prophage pi2 protein [Streptococcus pyogenes] >gi|50261625|gb|AAT72393.1| unknown [Streptococcus pyogenes] >gi|50903550|gb|AAT87265.1| unknown phage protein [Streptococcus pyogenes MGAS10394] + YP_060448 + 1039 + + + 1 + 146.36167621763 + 368 + 4.74132513340056e-33 + 50 + 227 + 655 + 832 + 0 + 0 + 78 + 112 + 0 + 178 + NEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWD + NEGFRTAVIEIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWN + NE FRT V W AI + IS ++ + +F+M +WG + WW ENQ LI+ ETVWNAI TV++TVM+ + P ++ AW I ++TT +IKTVV+T + VVLGIIKA+MQ I GDWSGAWET+KGV +W+ I+ +V + + Q +K+ + + I +V IW+ + + + + + 8 + gi|29374987|ref|NP_814140.1| + tail protein [Enterococcus faecalis V583] >gi|29342445|gb|AAO80211.1| tail protein [Enterococcus faecalis V583] + NP_814140 + 1049 + + + 1 + 139.0428842752 + 349 + 6.84844401007043e-31 + 73 + 482 + 545 + 920 + 0 + 0 + 110 + 196 + 78 + 432 + EAVVSFVMDLWGQMVAWWNENQELIRQ-------TAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVL----NVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSIS-----------NALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGF + DSIVKTASGLKGSLVKTWNDITAKVSEIWKKFTDAGKKTFDGFKKTVENVFNGIKNFLQTVWNVIYAVVGAIIVNTINIWKGIFDG--------FKAYFQYL-------WDLIKAIATGVWEKIGDTVTGIINGFIGVIKGIFDAFKTFFQQIWDAVVYSVTIAWNGIKNTVTSVSTAIKNFVTPIFNAIKTTITNVFNAIKNTATNVWNAIKTTISNVVQTILNF---------------------------------VTPIFNTMKNTITNIFNAIRNTASSVWNSIKTTISNIVTSVKNTVINIFNALKNSITNIFNAIRNTASTVWNSIKSTVSNIVSATVNTVKNLFNGMKNTVSSIWDGVRNTISNVVNAVKNTISNVWGGITGTVSN----IFNGVKNAIDGPMNAAKNLVKNVV----DAIKGF + +++V L G +V WN+ + + + ++ + VE V + +QT W++I AVV ++ N+ K + D KA Q + W+ +K +A +WE I V I+G + + + K+ + +W ++ V W+ IK TV++ TA+ + I +I+TT V+NAI A+N+W AI TT+ +V+ TI + VT F+ +K I+N + I+ S +WN+I T +S I +K + +K +I+N+ I++ T WN+IK+++S N N +K+ + W+ +++ IS + +K+T+SN W + TV+N I + V+ D +NAA+N + N + D I GF + + + + + 9 + gi|163941333|ref|YP_001646217.1| + prophage LambdaBa01, membrane protein, putative [Bacillus weihenstephanensis KBAB4] >gi|163863530|gb|ABY44589.1| prophage LambdaBa01, membrane protein, putative [Bacillus weihenstephanensis KBAB4] + YP_001646217 + 725 + + + 1 + 138.657684699283 + 348 + 8.15996781441799e-31 + 61 + 480 + 142 + 560 + 0 + 0 + 118 + 203 + 29 + 434 + WEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIK---AVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKT----VWS-------AAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLIN + WDAIKQWTIDAWNAIGEFLVGIWDGIVQWASEAWNSISESTSAVWNSIKEFLIGIWNGIVEFVVT-WGT--AILETYVGIWTSIFNFCMEIWNGIVEYLTSVLQGIATFFTEIWTSISTFFQEIWNGLVAFITPVLQGIADFFAM-----------IWNGISTVIQTVWNFITQYLQAIWTAILYFATPLFESIKNFISECWNKISSTTSLVWETIKNFLVSCWNGLVSFVTPIFEKIKSWIISVWDTISSATMAVWNAVKNFLQACWNGLVSIVTPIFDAIKNWIVNVWNAISSTTSAVWNAIKSYLSSLWNSIVSTASSIFNSIKSAISTVWNMISSASSSVWNGIKSTLSSIWNGIKSTASSVWNGLKDAIMTPVRWVTSAVSGAFNGMKSAVLGVWDGIKSGIRTAINGIIRIINKFI-DGFNTPAELLN + W+AIK A A+ F++ +W +V W +E I ++ VWN+I+ + + ++ V T W A++ T + + ++ + +++ GI++ +V+Q I ++ W ++ IW G+ + + + G+ F +W I V+ +W++I + TA+ + SI+ WN IS+ S +W I ++S + ++ E IK+ VW A W +K A +V +VT FD IK I N W I + TS +WNAI ++LS +W I + AS+ + IK+ IS V I S + WN IK+++S+ N IKS A + WN +K AI T + + S VS +N + S V I S +RT + + FI + + +L+N + + + + + + + 6589360 + -2041834015 + 0 + 504129014857 + 0.041 + 0.267 + 0.14 + + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/blastp_sample_converted.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastp_sample_converted.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,9 @@ +Sample gi|119953746|ref|YP_950551.1| 96.90 516 16 0 1 516 27 542 0.0 949 +Sample gi|148986157|ref|ZP_01819143.1| 41.27 252 115 3 49 300 679 897 2e-41 174 +Sample gi|77411259|ref|ZP_00787609.1| 41.00 261 143 2 50 310 655 904 8e-39 165 +Sample gi|76786754|ref|YP_329383.1| 39.46 261 147 2 50 310 655 904 7e-37 159 +Sample gi|153811333|ref|ZP_01964001.1| 29.98 557 277 18 3 516 573 1059 2e-36 157 +Sample gi|56962696|ref|YP_174422.1| 28.79 389 228 8 48 433 123 465 3e-33 146 +Sample gi|50914476|ref|YP_060448.1| 43.82 178 100 0 50 227 655 832 5e-33 146 +Sample gi|29374987|ref|NP_814140.1| 25.46 432 244 8 73 482 545 920 7e-31 139 +Sample gi|163941333|ref|YP_001646217.1| 27.19 434 287 7 61 480 142 560 8e-31 138 diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_rhodopsin_vs_four_human.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,10 @@ +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_rhodopsin_vs_four_human.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,741 @@ + + + + blastx + BLASTX 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + BLOSUM62 + 1e-10 + 11 + 1 + L; + + + + + 1 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 2 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 3 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 4 + Query_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + 1047 + + + 1 + Subject_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + Subject_4 + 348 + + + 1 + 639.032 + 1647 + 0 + 1 + 1044 + 1 + 348 + 1 + 0 + 336 + 343 + 0 + 348 + MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA + + + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + + + 5 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 33 + 183143 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 6 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 33 + 183143 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 7 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + + + 0 + 0 + 33 + 183143 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 8 + Query_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + 1574 + + + 1 + Subject_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + Subject_4 + 348 + + + 1 + 551.206 + 1419 + 0 + 42 + 1037 + 1 + 332 + 3 + 0 + 283 + 315 + 0 + 332 + MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE + MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S++GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF++QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+ + + + + + + + 0 + 0 + 33 + 183143 + 0.041 + 0.267 + 0.14 + + + + + 9 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + + + 0 + 0 + 40 + 509838 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 10 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + + + 0 + 0 + 40 + 509838 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 11 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + + + 0 + 0 + 40 + 509838 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 12 + Query_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + 4301 + + + 1 + Subject_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + Subject_4 + 348 + + + 1 + 220.705 + 561 + 3.21377e-67 + 1 + 333 + 11 + 121 + 1 + 0 + 107 + 109 + 0 + 111 + VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG + VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG + + + 2 + 127.487 + 319 + 1.95079e-35 + 3174 + 3368 + 248 + 312 + 3 + 0 + 60 + 64 + 0 + 65 + KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ + KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ + KEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ + + + 3 + 121.709 + 304 + 1.62516e-33 + 2855 + 3031 + 177 + 235 + 2 + 0 + 54 + 57 + 0 + 59 + RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS + RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA + RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE + + + + 4 + 97.0561 + 240 + 1.16473e-25 + 1404 + 1580 + 119 + 177 + 3 + 0 + 55 + 56 + 0 + 59 + LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR + LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR + L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR + + + 5 + 56.9954 + 136 + 1.23645e-12 + 4222 + 4299 + 312 + 337 + 1 + 0 + 23 + 24 + 0 + 26 + QFRNCMLTTLCCGKNPLGDDEASTTA + QFRNCMLTTICCGKNPLGDDEASATV + QFRNCMLTT+CCGKNPLGDDEAS T + + + + + + + 0 + 0 + 40 + 509838 + 0.041 + 0.267 + 0.14 + + + + + 13 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + + + 0 + 0 + 29 + 112346 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 14 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + + + 0 + 0 + 29 + 112346 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 15 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + + + 0 + 0 + 29 + 112346 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 16 + Query_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + 983 + + + 1 + Subject_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + Subject_4 + 348 + + + 1 + 589.341 + 1518 + 0 + 1 + 978 + 11 + 336 + 1 + 0 + 310 + 322 + 0 + 326 + VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT + VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T + + + + + + + 0 + 0 + 29 + 112346 + 0.041 + 0.267 + 0.14 + + + + + 17 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 18 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 19 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 20 + Query_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + 1047 + + + 1 + Subject_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + Subject_4 + 348 + + + 1 + 619.387 + 1596 + 0 + 1 + 1044 + 1 + 348 + 1 + 0 + 325 + 337 + 0 + 348 + MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA + + + + + + + 0 + 0 + 30 + 119944 + 0.041 + 0.267 + 0.14 + + + + + 21 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 32 + 155584 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 22 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 32 + 155584 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 23 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + + + 0 + 0 + 32 + 155584 + 0.041 + 0.267 + 0.14 + + + No hits found + + + 24 + Query_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + 1344 + + + 1 + Subject_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + Subject_4 + 348 + + + 1 + 532.717 + 1371 + 0 + 23 + 1021 + 1 + 333 + 2 + 0 + 272 + 307 + 0 + 333 + MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA + MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++ + + + + + + + 0 + 0 + 32 + 155584 + 0.041 + 0.267 + 0.14 + + + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_rhodopsin_vs_four_human_all.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human_all.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,10 @@ +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A 0 gi|57163782|ref|NM_001009242.1| gi|57163782|ref|NM_001009242.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 15KA71FL4TS79VA9ML34VI71LI7SASA21LI13TA1GV11 99 33 N/A N/A N/A N/A N/A +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 N/A 0 gi|2734705|gb|U59921.1|BBU59921 gi|2734705|gb|U59921.1|BBU59921 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 10IV1MF2KA20YF1IM1CA7LV7ML5IV17FV1NDHL4CG3VS1ML1ST1MLNH3IVLF1AP3YNVL36SG4VI7IV3SA2VA3LA9ML5VI26LM8RQ2CF30VIFA13FY2STNH3EN7VI7SASA9LM8IL2LI6FL1ED1DE 63 21 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 sp|P08100|OPSD_HUMAN 561 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 5KA9HY61FL4TS28 22 3 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 18LV3GS19LI7SASA13 22 2 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 304 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 2/0 6ML34VI14VARASA 22 1 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 3/0 1AG36LV1LF13VA4 22 1 N/A N/A N/A N/A N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 N/A 0 gi|283855845|gb|GQ290303.1| gi|283855845|gb|GQ290303.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 9LI13TA1AV 22 1 N/A N/A N/A N/A N/A +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 N/A 0 gi|283855822|gb|GQ290312.1| gi|283855822|gb|GQ290312.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 5KA66ND4FL4TS5ML7AP49LV25ML34VI40VI6LV19VI11SASA21LI13TA1 99 33 N/A N/A N/A N/A N/A +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A 0 gi|18148870|dbj|AB062417.1| gi|18148870|dbj|AB062417.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 1/0 15KA9AY22MV38FL4TS79VA9ML10PLHKEP1TV14IT2LM1VI47LV3GS11DN14TSSA1VI17VL2LI13TA13 99 33 N/A N/A N/A N/A N/A +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 N/A 0 gi|12583664|dbj|AB043817.1| gi|12583664|dbj|AB043817.1| 0 0 sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN sp|P08100|OPSD_HUMAN N/A N/A 2/0 10IV1MF22AQ2AM1SA4FL2IVAL12IVEQ23FL4TS1ML3ML12IL14CS8WYMV5VMTS6SN6MAVF2TV6LA3FA20RLAK1GEIV10TVCV2ST2LMAIVI1SF4RQ2CF12EA3RK2RK6VI4SA2VI9WF8TN9SA5SA1LI3MV3CM6HN2IL2LI6FLEGEDEDDEGA 74 25 N/A N/A N/A N/A N/A diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_rhodopsin_vs_four_human_converted.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,10 @@ +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,10 @@ +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 sp|P08100|OPSD_HUMAN 561 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 304 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_rhodopsin_vs_four_human_ext.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,10 @@ +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 3e-67 220 sp|P08100|OPSD_HUMAN 561 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 304 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 N/A +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 N/A +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 N/A +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 N/A +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 N/A diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_sample.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_sample.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,758 @@ + + + + blastx + BLASTX 2.2.24+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + /share/BlastDB/nr + Query_1 + phage_suis + 1890 + + + BLOSUM62 + 0.001 + 11 + 1 + L; + + + + + 1 + Query_1 + phage_suis + 1890 + + + 1 + gi|119953746|ref|YP_950551.1| + tail tape measure protein [Streptococcus phage SMP] >gi|118430558|gb|ABK91882.1| tail tape measure protein [Streptococcus phage SMP] + YP_950551 + 659 + + + 1 + 988.407949172964 + 2554 + 0 + 336 + 1889 + 25 + 542 + 3 + 0 + 518 + 518 + 0 + 518 + NWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + NWFHLLNSGGSALSVMFAKLVGIIAGISAPIWAVIGVIAALVAGFVLLYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + NWFHLLNSGGSALSVMFAKLVGIIAGISAPIWAVIGVIAALVAGFVLLYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + + + + + 2 + gi|289551554|ref|YP_003472458.1| + Phage tail length tape-measure protein [Staphylococcus lugdunensis HKU09-01] >gi|289181085|gb|ADC88330.1| Phage tail length tape-measure protein [Staphylococcus lugdunensis HKU09-01] + YP_003472458 + 1220 + + + 1 + 256.91395450591 + 655 + 5.97108392092708e-66 + 342 + 1889 + 657 + 1106 + 3 + 0 + 170 + 254 + 66 + 516 + FHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + FTLLFGKASLVRTVFGLLVGVFTSLSAPVLAVIAVIGSLVAIFVYLWKTNDGFREACINAWNVIKTTVSTVVTVIVAFVKSIWGGLVAWWQQNHVLIQAAATVVWNAIKTVIMTVMNALGPSMKTAWEVIKQAVIIVWEFIKTYVQVAIAVVSGVIKTVMQLITGDWSGAWNTIKQTAMTVWNLIKS-------GATAIFNA----LKVALSAIWNAIKSAASGAWNDMKAVIVAAVNYIKNRVQAQWNTLKAITTGVWNGIKAVISAVWNAIKSFVTSSVSKVKSSVSSGFNSVRNV-------VRSVMSA---------------VKSFISSAWNGVKSIVSGAVGAVKSFVSSGFNAVRNTVSSIMSRVKGIISSI-----------WNSIKSTVSNAVHNMTSA----------------------MSSGMSRMGSAVHSGMSRVSSAVRNGISGAYNAVRGGVYRMVSAGADLARGIARGIMNMAGYVMSRARALASRAVSAIKSALRIHS + F LL S + +F LVG+ +SAP+ AVI VI +LVA FV L+ TN+ FR AW IK+ +ST V +V+FV +WG +VAWW +N LI+ A VWNAI+TV+ TVM AL P ++TAW++I V V IKT V + VV G+IK VMQ+I GDWSGAW T+K A T+W IKS G IF LK +W I + W+ +K + A+ + +Q +++ VWN I V S +W AI + V S ++ + + + ++ V +++V +A +K IS+AW +K+ S A+ +F+S + ++ S+ +K IS++ WN+IK+++SNA++N+ SA +S+G + + S V + R+ SAVR G A NA R + +S G DL G G+ AG ++ S A+ K L I S + + + + + 3 + gi|223044325|ref|ZP_03614360.1| + phage tape measure protein [Staphylococcus capitis SK14] >gi|222442293|gb|EEE48403.1| phage tape measure protein [Staphylococcus capitis SK14] + ZP_03614360 + 1320 + + + 1 + 252.67675917082 + 644 + 1.12609769207128e-64 + 393 + 1889 + 655 + 1193 + 3 + 0 + 165 + 275 + 54 + 546 + LVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTA---ETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLV---------------QVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVG-------PIWDWIKTT-------VSNAITAVWEIIQNIMTSIQTTW----DTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVS-----------AVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGIKS + LGGVLAALSGPVGIVIAAVAAVIAIFVALWNSSETLRNALTDAWNAIASSVGAAIQAVLGFLGDLFGRA-------QEILAPLAPMFQQVWSQIVAIVDTAVNVIAPMVKQAFNTVVAVVKVAWEIIKAVIKISMEVILSTIVALLQLLTGDWRGAWQTMSKAGAEIWKAIVEMAKNIWSILGDYLKQSWQNIVDGFSAIFGPLAGIAGSIWNGIVNIVKTVVSGLGAFLTSIWTAIVTSAQVQWSIIATVAQTIWSAIVNVIVTVVTTLVSILATIWTTIVTVASTIWTTLVTVSQTIWTIIVTTITTIVTTLGTILSAIWTGIVTVATTIWTTLVTVAQTIWTLIVTTITTIISTLVTIITTVWTTIVSVTSTIWSSLVAIAQTIWSSVLSIISGIVGVIVAIVTGNWSLLRSSTASIMSGIAGLISAVWNSITSVISSAVSNAVSTAVSGFFNMLSSIGSAMHGIVSSVLSGMMSVVNSVRSGVSNALSAVRNFIGHFTQAGTDLIMGMVNGIKNAAINVVNAAKGVASSAINAVRSVLNSHS + L G++A +S P+ VI +AA++A FV L+N++E R + AW AI S++ A++AV+ F+ DL+G+ QE++ A + VW+ I +V+T + + P+V+ A++ ++AVV +IK V+ ++V+L I A++Q++ GDW GAW+T+ IW+ I + Q +DG IF SIW+ + + VV IW I T+ ++ +W I N++ ++ TT T+W I TVAS IWT + T ++ T I I T + + T+ SA W I V I T+V + + LI I+ + T + +W I + S IW + A T W + + IS ++ I + + W+ +++S ++ ++ I WN+I S IS+A+ N ST +G+ N++S++ +A IVS +VR+G NA++A RNFI + G DLI G V G+K AA +++A G S AI+ + +L S + + + 2 + 130.568493605019 + 327 + 6.45396672852224e-28 + 384 + 1796 + 844 + 1309 + 3 + 0 + 101 + 215 + 79 + 508 + FAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVM----QMINGDWSG-------AWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMS-VLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKS--------------------NIETAWNNIKTSISNALNNIKSAAENAWNNIKSAI--STAIENIKSTVSNG---WNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEG + FSAIFGPLAGIAGSI-------------------------------WNGIVNIVKTVVSGLGAFLTSIWTAIVTSAQVQWSIIATVAQTIWSAIVNVIVTVVTTLVSILATIWTTIVTVASTIWTTLVTVSQTIWTIIVTTITTIVTTLGTILSAIWTGIVTVATTIWTTLVTVAQTIWTLIVTTITTIISTLVTIITTVWTTIVSVTSTIWSSLVAIAQTIWSSVLSIISGIVGVIVAIVTGNWSLLRSSTASIMSGIAGLISAVWNSITSVISSAVSNAVSTAVSGFFNMLSSIGSAMHGIVSSVLSGMMSVV--------NSVRSGVSNALSAVRNFIGHFTQAGTDLIMGMVNGIKNAAINVVNAAKGVASSAINAVRSVLNSHSPSRVMMGIGGDFGEGFKIGIDDKKKSVANIAGGLGSSAVKA---VKNAVNPTDVLSDVRSTLKNSNLKIPNIQGDIKNASASANANITHTHEYKTNPSQRVVTVQMDVNNDALTHIVNG + F+ + G +AGI+ I W I + + T V + +F+ +W +V +I A+T+W+AI V+ TV+T L+ I+ T W I+ V +T+ + TV T +++ I ++ +++ W+G W TL VA TIW I + + I LV I T + S+ T+W +++A+ IW + + +S + + I+ + ++++ ++ + I+ + S +W +I++ + S V + + + ++ ++ SA I+ +V + ++ + + ++ +SNA ++ A T + G+ GIK AA K S+ + ++S + ++ K S++N + S+A A +K+A+ + + +++ST+ N N+ + NA + + + N ++ ++ + V D + V G + + + + + 4 + gi|268611153|ref|ZP_06144880.1| + hypothetical protein RflaF_16865 [Ruminococcus flavefaciens FD-1] + ZP_06144880 + 1158 + + + 1 + 239.194774013712 + 609 + 1.28842161409548e-60 + 78 + 1847 + 440 + 1042 + 3 + 0 + 183 + 291 + 85 + 639 + NLVAGLGQKDADIKGLLSNLGETIQNFVRNVKNVVLTIWDNL-PLAPWQKW----LGLIAVAAGPFLMLLGXXXXXXXXXXXXXXXXXXXXNWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVW-----------NAISTVASNIWTAISTTVMSVLTTIWGYIQT---------------YLELIKTVWSA------------------AWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS + NLGGQLTILKSQLQELAISFGEILMPAIRAIVSKIQGFIDKLNAMDPATKETIVKIALVAAALGPLLVVVGKTMVGVGKLMQLVANLPT-------IIAGAKAAFTSFGAAIG---GISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWNQIKSIFDNFCQGIVDRVNAL--------GFDFKNISEVIKAVWDGL-------CKFLAPVFE-------GVFQQVANIFKAVTD----IILNILDIFVGIFTGDWSRVWDGIKGIFVAVWNFLKDTLKNYLNVLCNLFGTNLDEVKEFWVNVWTSIKNFFVNIWNGIKNFITGVVNAIKNFFTTIWTGIKNFFVGIWTAIYNSVAEKINLIKTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNTIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLASQAFQWGADIINGIVNGIKNCIGKVADAVKGVAN + NL L + ++ L + GE + +R + + + D L + P K + L+A A GP L+++G + ++ + + + + +G A F +G GISAP+ AVI V+AALVA FV L+ TNE+FR K+ A W IKS + +V V L + + I + + VW+ + L P+ + V V N+ K V D ++L I+ + + GDWS W+ +KG+ +W +K ++ ++ L +F T L +K W VW +I IW+ IK ++ + A+ I T I+ + +W N I TV + +W AI T + VL IW I T + L +T++ A AWE IKAV +L I ++ ++ I AI+ + I S +WNAI++F+SG+ I + S+ W IK I+N + I + + WN I IS LN I S + WN IK+ ++ + IK+TVSN W+++ + VT I + GF+ AVN +N S A G D+ING V G+K G++ DAV G + + + + 2 + 141.354081730704 + 355 + 3.65629455324605e-31 + 543 + 1856 + 547 + 938 + 3 + 0 + 103 + 183 + 52 + 441 + ISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNL---VSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAI + ISAPVVAVIAVVAALVAAFVHLWRTNEDF-RNKITAIWNQIKSIFDNFCQGIVDRVNA-------------------LGFDFKNISEVIKAV-------WDGLCKFLAPVFEGVFQQVANIFKAVTDIILNILDIFVGIFTGDWSRVWDGIKGIFVAVWNFLKDTLKNYLNVLCNLFGTNLDEVKEFWVNVWTSIKNFFVNIWNGIKNFITGVVNAI-----------KNFFTTIWTGIKNFF-------VGIWTAIYNSVAEKIN----LIKTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFI + IS V AV++ V L V W N++ R +WN I+++ + ++ V + K + +IKAV W G + L V +++ + ++ + D ++ I + W VW I + +W+++K T+ N + + + + ++ W VW +I NIW I + V+ I K ++ W IK F VG+ T ++ + + I+ +IKT + +WNAI T +S + I ST W+ I IS ++ + ET + I IS ++ I AW NIK+ ++ +E IKS + WN + ++TV +A ++S V + ++ N I + IS + I + A ++ AV A+SG I + + + 3 + 140.198483002952 + 352 + 8.14537447802119e-31 + 522 + 1844 + 722 + 1121 + 3 + 0 + 116 + 190 + 77 + 459 + WEAIKSAISTAVEAVVSFVMDLW--------GQMVAWWN---ENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSN--GWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLI-----NGFVEGVKGAAGRLIDAVGGAV + WNGIKNFITGVVNAIKNFFTTIWTGIKNFFVGIWTAIYNSVAEKINLIKTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAI----HTAIT-------TVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAIS-----------GFISGVLNTISSVVSSIWNGIKNTVTNILNTIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNF-------IKNLASQAFQWGADII---------------NGIVNGIKNCIGKVADAVKGVANKIKSFLHFSVPD-EGTLADFESW--------------MPDFMQGLAQGINKSKKYVEKAISGVADAMTIAMNSDFNVDMSGVTGAMVGAGGTTV + W IK+ I+ V A+ +F +W G A +N E LI+ VWNAI T + V+ A+ ++ T W I ++ +L + + +T + + II VM I+ + AWE +K V + E IKS+++ + + T + TV I V+ +W+ I + +S + A+W +I +I SI+ NAI V S +W AIS G+I L I +V S+ W IK IL TI V+ +D +K A++ IK +NA F IK AS A++W I N I I N + + A + N IKS + ++ + + T+++ W + G +N ++ ++ AIS D + + F + G G ++ A G V + + + 4 + 115.160510568324 + 287 + 2.80602663410135e-23 + 501 + 1694 + 770 + 1144 + 3 + 0 + 100 + 176 + 39 + 406 + RTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWET----LKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENI-KSTVSNGWNNLVSTV---TNAGPRIVS + KTVITVVWNAIHTAISMVLNAIWNVISTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVL--------NTISSVVSSIWNGIKNTVTNI-------LNTIKTTVSNIWDSVKNAVTQKITAI-------KDTIVNGFNAAVNFIKNLASQAFQWGADIINGIVNGIKNCIGKVADAVK----GVANKIKSFLHFSVPDEGTLAD-----FESWMPDFMQGLAQGINKSKKYVEKAISGVADAMTIAMNSDFNVDMSGVTGAMVGAGGTTVVNNYNNDNSRTVNQTNNSPKSLS + +T + W AI +AIS + A+ + + +W + + + E R ET++ AI ++ VM + + TAW+ I AVVT VL IK+V++T + I VM I+ S W + GV IW I S+ D + A + ++W+ + G I V+ T+S+ ++++W I+N +T+I N I T SNIW ++ V +T I + I ++AA IK + + ++ G + IK I + +K + N I +FL T A ++ + + M + I + ++ +IS + + A + +N S ++ A+ +TV N +NN S TN P+ +S + + + 5 + 90.8929372855311 + 224 + 5.66707902872949e-16 + 492 + 1148 + 811 + 1044 + 3 + 0 + 67 + 106 + 29 + 241 + EEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDT-----------GLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWD-----------WIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNI + EAFRYLFETIFEAIHVIISRVMDWIHEKITTAWENIKAVVTIVLEAIKSVIETVWNAIHTAITTVMDAISNVISTVWNAISSFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTV-------TNILNTIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLASQAFQWGADIINGIVNGIKNCIGKVADAVKGVANKI + E FR + +EAI IS ++ + + W + A E I+ ETVWNAI T + TVM A+ ++ T W+ I + ++ V+N I +V+ + L + ++ AV I+G SG T+ V +IW GIK+ V I T + +IWD+V + + I D +IK S A +II I+ I+ V +A+ VA+ I + + + 6 + 51.9877801178785 + 123 + 0.000291728300853117 + 1158 + 1883 + 547 + 775 + 3 + 0 + 50 + 102 + 35 + 253 + ISTTVMSVLTTIWGYIQTYLELIKT------VWSAAWEIIKAVFAAILLTIVGLVTG-NFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTI----KSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGI + ISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWNQIKSIFDNFCQGIVDRVNALGFDF-----KNISEVIKA----VWDGLCKFLAPVFEGVFQQVANIFKAVTDIILNILDIFVGIFTGDWSRVWDGIKGIFVAVWNFLKDTLKNYLNVLCNLFGTNLDEVKEFWVNVW---------------TSIKNFFVNIWNGIKNFITGVVNAIKNFFTTIWTGIKNFFVGIWTAIYNSVAEKINLIKTVITV + IS V++V+ + + ++ L +T +A W IK++F IV V FD N E+IK +W+ + FL+ ++EG+ + ++ + I N++ + W+ IK N +K +N N + + T ++ +K N W ++++ F N N +NFI+ ++ + G+K + A+ +V+ I+ K ++ + + + + + + 5 + gi|268610688|ref|ZP_06144415.1| + hypothetical protein RflaF_14482 [Ruminococcus flavefaciens FD-1] + ZP_06144415 + 1444 + + + 1 + 234.572379102704 + 597 + 3.17349283264528e-59 + 78 + 1847 + 440 + 1042 + 3 + 0 + 185 + 294 + 85 + 639 + NLVAGLGQKDADIKGLLSNLGETIQNFVRNVKNVVLTIWDNL-PLAPWQKW----LGLIAVAAGPFLMLLGXXXXXXXXXXXXXXXXXXXXNWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVS-------NAITAVWEIIQN----IMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQT---------------YLELIKTVWSA------------------AWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS + NLGGQLTILKSQLQELAISFGEILMPAIRSIVSRIQGLIDKFNALSPATKETIVKVALVAATLGPLLVVVGKTMVGVGKLMQLVA------NLPTIIASAKAA----FTSFGAAIGGISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWEQIKSIFSGFCQGIVDRINALGFDF---------------KNITEVIKAVWDGLCKFLKPIFEGQFQ-------QIANIFKAVTD----IILSVLDIFVGIFTGDWSRVWDGIKGIFVAVWNFIKDTLKNALNMICGIFGTDLGEVKEFWVGVWTSIKNFFVNIWNGIKNFISSVLGGIKNFFTTIWTGIKNFFVGIWTAIYSSVSEKINLIKTVITVVWNAIHTAISTVLNAIWSVITTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHDKIVERWETIKAIVTVVLEAIKSVIETVWNAIHTAISTVMDAIHNVVSTVWNAISGFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKGVAN + NL L + ++ L + GE + +R++ + + + D L+P K + L+A GP L+++G + ++ + + N ++ S +A F I GISAP+ AVI V+AALVA FV L+ TNE+FR K+ A WE IKS S + +V + L + + I+ V + + L PI + + + N+ K V D ++L ++ + + GDWS W+ +KG+ +W IK ++ A++ + IF T L +K W VW +I IW+ IK +S N T +W I+N I T+I ++ N I TV + +W AI T + +VL IW I T + L +T++ A WE IKA+ +L I ++ ++ I AIS + I S +WNAI+ F+SG+ I + S+ W IK I+N + I + + WN I IS LN I S + WN IK+ ++ + IK+TVSN W+++ + VT I + GF+ AVN +N S A G D+IN V G+K G++ DAV G + + + + 2 + 167.932852469002 + 424 + 3.64782449590402e-39 + 501 + 1856 + 770 + 1245 + 3 + 0 + 121 + 216 + 54 + 491 + RTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWET----LKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLT----TIWGYIQTYLELIKTVWSAAW----EIIKAVFAAI---LLTIVGLVTGNFDLIKQ------------AISNAW---------EIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGW---NNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAI + KTVITVVWNAIHTAISTVLNAIWSVITTVWQTIYDFISPLLEAFRYLFETIFEAIHVIISRVMDWIHDKIVERWETIKAIVTVVLEAIKSVIETVWNAIHTAISTVMDAIHNVVSTVWNAISGFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVL--------NTISSVVSSIWNGIKNTVTNI-------LNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKGVANKIKSFLHFSVPDEGPLADFESWMPDFMQGLADGINANTSVVNDAVNSFAGGLAEKISSVIQNALSNVVTSVQGFMTQVFDTVKTVWTNANAAIDATMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLDIKSVVTTTWEAVSGVVRTAVNAIKSVVQAVWDAMPDTV + +T + W AI +AIST + A+ S + +W + + + E R ET++ AI ++ VM + + W+ I A+VT VL IK+V++T + I VM I+ S W + GV IW I S+ D + A + ++W+ + G I V+ T+S+ ++++W I+N +T+I NAI T SNIW ++ V +T TI + IK + S A+ +II + + I + + V G + IK A +W + I TS + +A+ +F G+ E I + A + T++ MT + ++T W N +I ++ I S + W I S I TA+ENI++ ++ W ++++S + +IV+ V T N + + I + ++ + ++G V A ++ AV A+ + + + + 3 + 161.769659254324 + 408 + 2.61420693292496e-37 + 492 + 1832 + 811 + 1322 + 3 + 0 + 123 + 220 + 75 + 517 + EEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDT-----------GLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAI--------------------------DGLVQIFQTGLAFLKSIWDTV--WGT---------IMAVVGPIWDWIKTTVSNAITAV----------------W--EIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMS----VLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAV + EAFRYLFETIFEAIHVIISRVMDWIHDKIVERWETIKAIVTVVLEAIKSVIETVWNAIHTAISTVMDAIHNVVSTVWNAISGFISGVVNAIWSVISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKG-VANKIKSFLHFSVPDEGPLADFESWMPDFMQGLADGINANTSVVNDAVNSFAGGLAEKISSVIQNALSNVVTSVQGFMTQVFDTVKTVWTNA----NAAIDATMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLDIKSVVTTTWEAVSGVVRTAVNAIKSVVQAVWDAMPDTVRSAMNRVKEAVLSIWDGIKSGIGDRLGGVRDAVVNAMNAVYKAVKDKVNSSWSWGRDLMQNLINGITYMLGSLINTV + E FR + +EAI IS ++ + +++ W + A E I+ ETVWNAI T + TVM A+ +V T W+ I ++ V+N I +V+ + L + ++ AV I+G SG T+ V +IW GIK+ V + D +V F + F+K++ WG I +G + D +K V+N I + W + +Q + I V +A+++ A + IS+ + + V+T++ G++ + +KTVW+ A A A + I +T + I I A E I+ + W A+++ +S +GIK + W +K I IKS + T W + + A+N IKS + W+ + + +A+ +K V + W+ + S + + + AV + A ++ ++++ S G DL+ + G+ G LI+ V + + + 4 + 123.249701662589 + 308 + 1.03039235764918e-25 + 510 + 1859 + 905 + 1377 + 3 + 0 + 108 + 204 + 63 + 493 + VQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAV--------MQMINGDWSG-------AWETLKGVAGTIWEGIKSLVQVAI--DGLVQIFQTGLA-FLKSIWD-------TVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVT------------GNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLIN------GFVEGVKGAAGRLIDAVGGAVSGAID + ISSIWNSIKDHITNTLNAIHAVVSAVWNAISGFISGVLNTISSVVSSIWNGIKNTVTNILNAIKTTVSNIWDSVKNAVTQKITAIKDTIVNGFNAAVNFIKNLGSQAFQWGADIINNIVSGIKNCIGKVADAVKGVANKI----KSFLHFSVPDEGPLADFESWMPDFMQGLADGINANTSVVNDAVNSFAGGLAEKISSVIQNALSNVVTSVQGFMTQVFDTVKTVWTNANAAIDATMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLD-IKSVVTTTWEAVSGVVRTAVNA-----------IKSVVQAVWDAMPDTVRSAMNRVKEAVLSIWDGIKSGIGDRLGGVRDAVVNAMNAVYKAVKDKVNSSWSWGRDLMQNLINGITYMLGSLINTVA----DVARSIWEYLHFSVPEKGALTDVEEWMPDFMKGLAKGINKSKKYVEAAVSGVAD + + + W +IK I+ + A+ + V +W + + + I ++WN I+ V ++ A+ V WD + VT + IK + G + IK + +IN SG + +KGVA I KS + ++ +G + F++ + F++ + D V + + G + + I + + NA++ V +Q MT + T TVW + + IS+ + S TI I+T LE I+ V + W+ + +V +A L I +VT G D IK ++ WE + NA IK+ W+ + T+ + M +K + + W+ IK+ I + L ++ A NA N + A+ + + S + NL++ +T +++ V + + ++ ++ G L + F++G+ + V AVSG D + + + 5 + 71.6329584896635 + 174 + 3.55787431696712e-10 + 486 + 1343 + 1138 + 1400 + 3 + 0 + 60 + 128 + 35 + 292 + TNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTV--MSVLTTIWGYIQTYLELIKTVWSAAWEIIKA----VFAAILLTIVGLVTGNFDLIKQAISN + TMSQISSGITSGWKTIVSTIKTALENIRNVITTTWKAVSSVISAALDGIKKIVTVVWTALKNLIKTGQLDIKSVVTTTWEAVSGVVRTAVNAIKSVV-----------QAVWDAMPDTVRSAMNRVKEAVLSIWDGIKSGIGDRLGGVRDAVVNAM-------NAVYKAVKDKVNSSWSWGR-----------DLMQNLINGITYMLGSLINTVADVARSIWEYLHFSVPEKGALTDVEEWMPDFMKGLAKGINKSKKYVEAAVSGVADAMTLTMQSGLNVDMDGISGAMMN + T + + + + W+ I S I TA+E + + + W + + + + I++ VW A++ +++T + +V T W+ + VV T +N IK+VV +AV + A +K +IW+GIKS + + G+ + + V+ + V W W + +++QN++ I ++ N ++ VA +IW + +V LT + ++ +++ + + + + ++A V A+ LT+ + + D I A+ N + + + 6 + 53.9137779974652 + 128 + 7.67706873813937e-05 + 894 + 1883 + 467 + 775 + 3 + 0 + 73 + 133 + 43 + 341 + IKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKT------VWSAAWEIIKAVFAAILLTIVGLVTG-NFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTI----KSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLLGI + IRSIVS-RIQGLIDKFNALSPATKETIVKV-ALVAATLGPLLVVVGKTMVG-VGKLMQLVANLPTIIASA-----KAAFTSFGAAIGGISAPVVAVIAVVAALVAAFVHLWRTNEDFRNKITAIWEQIKSIFSGFCQGIVDRINALGFDF-----KNITEVIKA----VWDGLCKFLKPIFEGQFQQIANIFKAVTDIILSVLDIFVGIFTGDWSRVWDGIKGIFVAVWNFIKDTLKNALNMICGIFGTDLGEVKEFWVGVW---------------TSIKNFFVNIWNGIKNFISSVLGGIKNFFTTIWTGIKNFFVGIWTAIYSSVSEKINLIKTVITV + I+S+V I GL+ F K V + A +GP+ + T+ + + +++ N+ T I + A T IS V++V+ + + ++ L +T +A WE IK++F+ IV + FD N E+IK +W+ + FL I+EG + ++ + I +V+ + W+ IK N IK +NA N I T + +K W ++++ F N N +NFIS+ + + G+K + A+ +VS I+ K ++ + + + + + + 6 + gi|153811333|ref|ZP_01964001.1| + hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174] >gi|149832460|gb|EDM87544.1| hypothetical protein RUMOBE_01725 [Ruminococcus obeum ATCC 29174] + ZP_01964001 + 1228 + + + 1 + 219.934795217844 + 559 + 8.08889755547188e-55 + 108 + 1847 + 493 + 1073 + 3 + 0 + 176 + 285 + 81 + 621 + ADIKGLLSNLGETIQNFVRNVKNVVLTIWDNL-PLAPWQKW----LGLIAVAAGPFLMLLGXXXXXXXXXXXXXXXXXXXXNWFHLLNSGGSALSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKT-------TVSNAITAVWE-IIQNI---MTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELI----KTVWS-------AAWEIIK-AVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIW------------EGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTS-ISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS + SQLQELAISFGEILMPKIRDIVTHIQNFVDKLNAMDEGQKETILRIGMFVAALAPMLMGLGKVITFSANVSRALGTLSAG-----LVKAGG--FSGVFTKALGLI---TSPAAIVVGVIAAITAVIIHLWNTNEDFRNTITAIWQKIKDAFTTFAAGI---------------SERLSALGITFSDVTSAIKTIWDGFCNLLAPVLEAAFSTIAIALQTAFNVI-----------LGIWDVFSAVFSGDWSGAWEAIKGIFSSIWDGLKEYFSTIIGAVKGVADVFLGWFGTNWETVWNGVKTFFEGIWNGISSFFEGIWNGISTFCTTVWNGIVTNVTAFCTTVHDTISTIFNAVKDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTT----IWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATS + + ++ L + GE + +R++ + D L + QK +G+ A P LM LG + + V +S L+ +GG S +F K +G+I ++P V+GVIAA+ A + L+NTNE+FR + A W+ IK A +T + +E + T V +AI+T+ + L P+++ A+ I + T NVI LGI + +GDWSGAWE +KG+ +IW+G+K I + + L + + W+TVW + IW+ I + +S T VW I+ N+ T++ T T++NA+ V SN+W I V + I ++ ELI + +W + WE IK AV AI ++T + I I+ W I+T + + NAI + + W I T ST W IKTT + V+ IKS ++TAWN +K S I+ +N IK+ WN IK+A+ T + IK+TV +N + +TVT I +A++TG A NA + ++ I+ + + G+K + ++V A S + + + 2 + 195.667221935051 + 496 + 1.63364171761813e-47 + 519 + 1760 + 709 + 1099 + 3 + 0 + 127 + 197 + 51 + 428 + AWEAIKSAISTAVEAVVSFVMDLWGQM-------VAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWE-IIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQT-----YLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKT-SEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAIS + AWEAIKGIFSSIWDGLKEYFSTIIGAVKGVADVFLGWFGTNWE-------TVWNGVKTFFEGIWNGISSFFEGIWNGISTFCTTVWNGIVTNVTAFCTTVHDTISTIFNAV-----------KDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTT----FTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVI-----------NAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRAITT----PINAAKTAVGNAIS + AWEAIK S+ + + + + G + + W+ N E TVWN ++T E + + + W+ I TTV N I T V V I + + K V +WE IK++VQVAI +V++ + + + +W + +W+ IK+ V AI V + II +M +I T TVWNAI T +T + + S + T W +++ + I T S W IK F ++ + IK A+ AW +K + + N I T ++ +W IKTA T IKTT+ V +K+ + T WN IKT S A N +K+A N KSA+++AI IKST+S+ WN++ S ++ I A+ T +NAA+ + NAIS + + + 3 + 169.473650772671 + 428 + 1.25373984602686e-39 + 498 + 1640 + 746 + 1096 + 3 + 0 + 115 + 178 + 50 + 391 + FRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLK-SIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWD--------TVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIK-TVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSN + FGTNWETVWNGVKTFFEGIWNGISSFFEGIWNGISTF-----------CTTVWNGIVTNVTAFCTTVHDTISTIFNAVKDVVSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAIN-----------FVKDNIITPVMNAISATITTVWNAIQTTFTTVINA-------IKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNA-----------IKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRAITTPINAAKTAVGN + F T + W +K+ + SF +W + + TVWN I T V T + + T ++ + VV+ V IK VV + ++ ++KA ++I + WE + ++WE IKS VQ AI+ F+K +I V I A + +W+ I+TT + I A I +++QT W+ V NAIST S +W I TT +V+ I +QT +K +V + IK V + I V + IK + + +KT + IWNA IKT STAW +KT ++ + KS + +A N IK++IS+ N++KSA + WN IK AI+T I K+ V N + + + 4 + 118.242107175663 + 295 + 3.31465838308759e-24 + 492 + 1256 + 854 + 1111 + 3 + 0 + 71 + 119 + 23 + 268 + EEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILA-VVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKG------------VAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEI + ENCRDTIISVWETIKSAVQTAINFVKDNII----------TPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRAITTPINAAKTAVGNAISAIRSKFNFSWSL + E R + + WE IKSA+ TA+ V ++ I T TVWNAI+T TV+ A+ VQTAW+ + VVT V+N I T + T + V+ I AW +K V T+W IK+ VQ ++ + QT +K+ T+W I W+ +KT V+ I A + + + I++T +VWN++ + S+ W AI + + + + + I++ ++ +W + + + + 5 + 116.316109296076 + 290 + 1.25956884194974e-23 + 510 + 1385 + 816 + 1110 + 3 + 0 + 83 + 132 + 25 + 306 + VQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVET------------VMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVL-GIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQ-IFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWN + VSNVWETIKNVVQVAIMFIVEVVKAAFELITVPFRFIWENCRDTIISVWETIKSAVQTAINFVKDNIITPVMNAISATITTVWNAIQTTFTTVINAIKSAVQTAWNFMKDNVVTPVMNAISTTISTVWNTIKTTFTTVINAIKSAVQTAWNFMKNSVITPVMNGIKTVITTVWNAIKTAVQTVVNAIKTTVQTVFNAVKTTVTTIWNAIKTGTSTAWNAVKTAVTTPINAAKSAVTSAINGIKSTISSVWNSVKSATSSTWNAIKRA-----------ITTPINAAKTAVGNAISAIRSKFNFSWS + V WE IK+ + A+ +V V + + + E R T +VW I++ V+T VM A+ + T W+ I TTV+N IK+ V T + ++ VM I+ S W T+K T+ IKS VQ A + + + + +K++ TVW I V + + IKTTV AV + I +I+T T WNA+ T + A + V S + I I + +K+ S+ W IK +T + K A+ NA I++K + W+ + + + + + 7 + gi|262113750|emb|CAR95417.1| + hypothetical protein [Streptococcus phage phi-m46.1] + CAR95417 + 952 + + + 1 + 218.779196490092 + 556 + 1.80201837527491e-54 + 384 + 1241 + 540 + 818 + 3 + 0 + 110 + 166 + 7 + 286 + FAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS + FLPIVGIIVGIVAAI-------TLLIVGLKELWTNHEGFRTAVTEIWNSIYAFLSMIIQQISSFVMSVWGTLTTWWTENQQLILNAATTVWNAITTVIQTVMTILGPLIQASWENIKLIITAAWEMIKIVVETAINVVLGIIKAVMQVITGDWTGAWETIKQVLSMAWEGIKSLISLALNFIAQYISTAWTGIKNTISNVLSAISSVISSIWTAIQSTISSVLSAIGSTVSTIWNGISNTVSNILNGISNTVSSVWNGVKNTISNAINGARDAVSNAINAIKNLFN + F +VGII GI A I L+ G L+ +E FRT V W +I + +S ++ + SFVM +WG + WW ENQ+LI A TVWNAI TV++TVMT L P++Q +W+ I ++T +IK VV+T + VVLGIIKAVMQ+I GDW+GAWET+K V WEGIKSL+ +A++ + Q T +K+ V I +V+ IW I++T+S+ ++A+ + I I T + N IS S++W + T+ + + + + IK +++ + + + 2 + 171.784848228175 + 434 + 2.526199638793e-40 + 657 + 1871 + 460 + 858 + 3 + 0 + 122 + 198 + 18 + 411 + NAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNV---IKTVVD--TGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG + NALAAIGQPILEMLIPVFQSLADIVSQLATWFTNLSSPIKEVVIIFTGILAVVGMLLPVFLGLQVAAAAMGTTVVGMITAFLPIVGIIV-----GIVAAITLLIVGLKELWTNHEGFRTAVT-EIWNSIYAFLSMIIQQISSFVMSVWGTLTTWWTENQQLILNAATTVWNAITTVIQTVMTILGPLIQASWENIKLIITAAWEMIKIVVETAINVVLGIIKAVMQVITGDWTGAWETIKQVLSMAWEGIKSLISLALNFIAQYISTAWTGIKNTISNVLSAISSVISSIWTAIQSTISSVLSAIGSTVSTIWNGISNTVSNILNGISNTVSSVWNGVKNTISNA----INGARDAVSNAINAIKNLFNFQIRWPHIPLPHF--RVSGSANPLDWLKGGIPRISIDWYAKG + NA+ + + ++ LIP+ Q+ D++ + T N+ IK VV TG+ V+G++ V + + T+ G+ + +V G+V + LK +W G AV IW+ I +S I + + ++ ++ T W I A+ +W AI+T + +V+T + IQ E IK + +AAWE+IK V + ++G++ +I + AWE IK S W I + +S I STAW IK TISNV++ I S I + W I+++IS+ L+ I S WN I + +S + I +TVS+ WN + +T++NA ++ R NA+NA +N + I + F V G+A L GG +IDW AKG + + + + + 8 + gi|77411259|ref|ZP_00787609.1| + tail tape meausure protein [Streptococcus agalactiae CJB111] >gi|77162685|gb|EAO73646.1| tail tape meausure protein [Streptococcus agalactiae CJB111] + ZP_00787609 + 1039 + + + 1 + 215.697599882754 + 548 + 1.52550005815421e-53 + 387 + 1241 + 628 + 905 + 3 + 0 + 106 + 170 + 7 + 285 + AKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS + APIVGIILGVIAVV-------ALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTITNAINGAKNAVSSAINAIKNLFN + A +VGII G+ A + A LV G L+ +E FRT V W AI + +S ++ + SFVM +WG + WW ENQ+LI A TVW AI TV++T+MT L P +Q +W+ I ++TT ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V T+WE IKSL+ + + + Q +K + +I +VV +W+ IK+T+S+ ++++ + ++ ++ T V + IS S++W + +T+ + + + + + IK +++ + + + 2 + 172.55524738001 + 436 + 1.48099780677056e-40 + 660 + 1871 + 548 + 945 + 3 + 0 + 114 + 199 + 12 + 407 + AIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVA--IDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG + AMAEMGDAIAATLAPILEILASLLQAVATWFSGLSEPVKQ--FIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVGIILGVIAVVALLVVGIQQLWQHHEGFRTAVT-EIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTITNA----INGAKNAVSSAINAIKNLFNFKIKWPHIPLPHF--SVSGSANPLDWLKGGLPKISIQWYAKG + A+ + + + L PI++ L+ AV T + + V V++G + A + ++ + + TI I + + I G++ + + ++ +W G AV IW+ I +S I + + +I ++ T W I A+ +WTAIST + +++T + Y+Q E IK + + AW+IIK V + ++G++ +I S AWE IK S +W AI + +S + I S +W IK T++N++ +IKS + WN+IK++IS+ L++I S + WN +K+ IS + I +TVS+ WN + ST+TNA ++ + +A+NA +N + I + F V G+A L GG +I W AKG + + + 3 + 83.5741453431014 + 205 + 9.04763716179523e-14 + 978 + 1877 + 540 + 882 + 3 + 0 + 81 + 141 + 67 + 355 + TVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVAS---------NIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGL--VTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKT-----------AASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAI-----------STAIENIKSTV----------------------SNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDWAKGLL + TAQNTAKLAMAEMGDAIAATLAPILEILASLLQAVATWFSGLSEPVKQFIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVG--------IILGVIAVVALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLSVIIQQISSFVMSIWGTLTTWWTENQQLILNAANTVWTAISTVIQTIMTILGPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEAIKSLISIVLSAIAQFISNSWNGIKGTMTN----LLNSIKSVVSNVWNSIKSTISSILSSIGSTVSSVWNGMKATISGVLSGISNTVSSVWNGVKSTI + T T + + D I T++ + + ++Q + T + V I V S I+ A+ M++ TTI G I ++ II V A + L +VG+ + + + + A++ W I S I I++F+ IW + T AA+T W I T I +MT + ++ +W NIK I+ A + IK E A N + I S A E IK V SN WN + T+TN +++++++ N N+ ++ IS+ +S G ++ G+K ++ + VS + K + + + + + + 9 + gi|76786754|ref|YP_329383.1| + prophage LambdaSa04, TP901 family tail tape measure protein [Streptococcus agalactiae A909] >gi|76561811|gb|ABA44395.1| prophage LambdaSa04, tail tape measure protein, TP901 family [Streptococcus agalactiae A909] + YP_329383 + 1039 + + + 1 + 213.386402427249 + 542 + 7.57097807573937e-53 + 387 + 1241 + 628 + 905 + 3 + 0 + 105 + 169 + 7 + 285 + AKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS + APIVGIILGVIAVV-------ALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTVSSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNAINGAKNAVSSAINAIKNLFN + A +VGII G+ A + A LV G L+ +E FRT V W AI + ++ ++ + SFVM +WG ++ WW ENQ+LI TVW AI TV++T+MT L P +Q +W+ I ++TT ++IK VV+T + VVLGIIKAVMQ+I GDWSGAWET+K V T+WE IKSL+ + + + Q +K + +I VV +W+ IK+T+S+ ++++ + +I ++ T V + IS+ S +W + +T+ + + + + + IK +++ + + + 2 + 164.851255861663 + 416 + 3.08806866621938e-38 + 660 + 1871 + 548 + 945 + 3 + 0 + 111 + 194 + 12 + 407 + AIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVA--IDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG + AMAEMGDAIAATLAPILEVIASLLQAVATWFSGLSEPVKQ--FIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVGIILGVIAVVALLVVGIQQLWQHHEGFRTAVT-EIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTVSSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNA----INGAKNAVSSAINAIKNLFNFKIKWPHIPLPHF--SVSGSANPLDWLKGGLPKISIQWYAKG + A+ + + + L PI++ L+ AV T + + V V++G + A + ++ + + TI I + + I G++ + + ++ +W G AV IW+ I ++ I + + +I ++ T W I + +WTAIST + +++T + Y+Q E IK + + AW+IIK V + ++G++ +I S AWE IK S +W I + +S + I S +W IK T++N++ +IK + WN IK++IS+ L++I S + WN +K+ IS + I STVS WN + ST+TNA ++ + +A+NA +N + I + F V G+A L GG +I W AKG + + + 3 + 115.160510568324 + 287 + 2.80602663410135e-23 + 543 + 1391 + 637 + 900 + 3 + 0 + 70 + 130 + 19 + 283 + ISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAI + VIAVVALLVVGIQQLW--------QHHEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLISIVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTV-----------SSIWNGMKATISGVLSGISSTVSFVWNGVKSTITNAINGAKNAVSSAINAI + + V +V + LW ++ E R +WNAI + ++ + V + W ++ T +I +T + +I+ +M ++ +WE +K + T W+ IK +V+ AI+ ++ I + + + W W TI VV +W+ IK+ +S ++A+ + I N I+ T + N+I V SN+W I +T+ S+L++I + S+ W +KA + +L I V+ ++ +K I+NA K S NAI + + + 4 + 82.4185466153494 + 202 + 2.01560327678347e-13 + 978 + 1847 + 540 + 850 + 3 + 0 + 74 + 133 + 45 + 323 + TVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVAS---------NIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGL--VTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKT-----------AASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAI-----------STAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVS + TAQNTAKLAMAEMGDAIAATLAPILEVIASLLQAVATWFSGLSEPVKQFIVIVGSLVAALGLVLPIFIALQAAAMAMGTTIMGMITAAAPIVG--------IILGVIAVVALLVVGIQQLWQHHEGFRTAVTEIWNAIYAFLTVIIQQISSFVMSIWGTLITWWTENQQLILNATNTVWTAISTVIQTIMTILAPYLQASWENIKLIITTAWDIIKVVVETAINVVLGIIKAVMQIITGDWSGAWETIKQVVSTVWEVIKSLIS----IVLSAIAQFISNSWNGIKGTMTNLLNSIKGVVSNVWNGIKSTISSILSSIGSTVS + T T + + D I T++ + + ++Q + T + V I V S I+ A+ M++ TTI G I ++ II V A + L +VG+ + + + + A++ W I + I I++F+ IW + T A +T W I T I +MT + ++ +W NIK I+ A + IK E A N + I S A E IK VS W + S ++ ++SA+ N+ N + ++N ++ +++ G+K ++ ++G VS + + + + + 10 + gi|50914476|ref|YP_060448.1| + unknown phage protein [Streptococcus pyogenes MGAS10394] >gi|40218580|gb|AAR83234.1| prophage pi2 protein [Streptococcus pyogenes] >gi|50261625|gb|AAT72393.1| unknown [Streptococcus pyogenes] >gi|50903550|gb|AAT87265.1| unknown phage protein [Streptococcus pyogenes MGAS10394] + YP_060448 + 1039 + + + 1 + 207.608408788489 + 527 + 4.15433379501178e-51 + 372 + 1241 + 623 + 905 + 3 + 0 + 104 + 166 + 7 + 290 + LSVMFAKLVGIIAGISAPIWXXXXXXXXXXXXXXXXYNTNEEFRTKVQAAWEAIKSAISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWS + LVVAAAPIVGTVLGIIAVI-------TLLVVWIQELWQNNEGFRTAVIEIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWNTIKSVISSVISSIVSFVSSGWSGIQQTISSILSGISSTVSSVWNGIKNSISNAINGAKNVVSSAINAIKNLFN + L V A +VG + GI A I LV L+ NE FRT V W AI + IS ++ + +F+M +WG + WW ENQ LI+ ETVWNAI TV++TVM+ + P ++ AW I ++TT +IKTVV+T + VVLGIIKA+MQ I GDWSGAWET+KGV +W+ I+ +V + + Q +K+ + + I +V IW+ IK+ +S+ I+++ + + + IQ T ++ + IS+ S++W I ++ + + + + + IK +++ + + + 2 + 155.221266463729 + 391 + 2.44682334507151e-35 + 660 + 1871 + 548 + 945 + 3 + 0 + 111 + 192 + 20 + 411 + AIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVA------IDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSGIWEGIKTAASTAWEWIKTTISNVMTTIKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTNAGPRIVSAVRTGFDNAVNAARNFISNAISVGGDLINGFVEGVKGAAGRLIDAVGGAVSGAIDW-AKG + AMAEVGGVLAEALAPVLELLAQLLQAVANWFSN-LPGPIQTFIVIMGGLITVVGLLLPGLLA-----LQAAAVAMGTTIGGLVVAAAPIVGTVLGIIAVITLLVVWIQELWQNNEGFRTAVI-EIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWNTIKSVISSVISSIVSFVSSGWSGIQQTISSILSGISSTVSSVWNGIKNSISNA----INGAKNVVSSAINAIKNLFNFKISWPHIPLPHF--SVSGSANPLDWLKGGLPKISIAWYAKG + A+ V + AL P+++ L+ AV N + + T + ++ G+I V ++ G + L+ A + I LV A + G++ + + +++ +W G AV+ IW+ I +S I + I I ++ T W I +W AIST + +V++ I Y++ I+ + + AWEIIK V + ++G++ I S AWE IK +W AI ++ I I S W IK T SN+++ I + + WN IK+ IS+ +++I S + W+ I+ IS+ + I STVS+ WN + ++++NA ++ + +A+NA +N + IS + F V G+A L GG +I W AKG + + + 3 + 121.708903358919 + 304 + 2.99798279087674e-25 + 543 + 1673 + 637 + 1004 + 3 + 0 + 89 + 168 + 29 + 387 + ISTAVEAVVSFVMDLWGQMVAWWNENQELIRQTAETVWNAIRTVVETVMTALIPIVQTAWDLILAVVTTVLNVIKTVVDTGLKVVLGIIKAVMQMINGDWSGAWETLKGVAGTIWEGIKSLVQVAIDGLVQIFQTGLAFLKSIWDTVWGTIMAVVGPIWDWIKTTVSNAITAVWEIIQNIMTSIQTTWDTVWNAISTVASNIWTAISTTVMSVLTTIWGYIQTYLELIKTVWSAAWEIIKAVFAAILLTIVGLVTGNFDLIKQAISNAWEIIKTKTSEIWNAITTFLSG--IWEGIK------TAASTAWEWIKTTISNVMTT--IKSNIETAWNNIKTSISNALNNIKSAAENAWNNIKSAISTAIENIKSTVSNGWNNLVSTVTN + IIAVITLLVVWIQELW--------QNNEGFRTAVIEIWNAIYAFISVIIQEISTFIMTIWGTLTTWWTENQALIQAAVETVWNAISTVIQTVMSLIGPYLEAAWANIQLIITTAWEIIKTVVETAITVVLGIIKAIMQAITGDWSGAWETIKGVLQRVWQAIQQIVTTILSAIGQFISNTWNGIKNTFSNILSAISGIVSSIWNTIKSVISSVISSIVSFV-----------SSGWSGIQQTISSILSGISSTVSSVWNGIKNSISNAINGAKNVVSSAINAIKNLFNFKISWPHIPLPHFSVSGSANPLDWLKGGLPKISIAWYAKGGILTKPTAFGMNEKQLMVGGEAGKEAVLPLTKQNLAAIGEGIASTMGTGGNFINVSITD + I + +V ++ +LW +N E R +WNAI + ++ + + T W + T +I+ V+T + +I+ VM +I AW ++ + T WE IK++V+ AI ++ I + + + W W TI V+ +W I+ V+ ++A+ + I N I+ T+ + +AIS + S+IW I + + SV+++I ++ S+ W I+ ++IL I V+ ++ IK +ISNA K S NAI + W I + ++ +W+K + + K I T + + ++ E K ++ E I ST+ G N + ++T+ + + + + + + + 12310662 + -87459526 + 0 + 1174893963300 + 0.041 + 0.267 + 0.14 + + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/blastx_sample_converted.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastx_sample_converted.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,33 @@ +phage_suis gi|119953746|ref|YP_950551.1| 100.00 518 0 0 336 1889 25 542 0.0 988 +phage_suis gi|289551554|ref|YP_003472458.1| 32.95 516 280 6 342 1889 657 1106 6e-66 256 +phage_suis gi|223044325|ref|ZP_03614360.1| 30.22 546 327 7 393 1889 655 1193 1e-64 252 +phage_suis gi|223044325|ref|ZP_03614360.1| 19.88 508 328 9 384 1796 844 1309 6e-28 130 +phage_suis gi|268611153|ref|ZP_06144880.1| 28.64 639 371 11 78 1847 440 1042 1e-60 239 +phage_suis gi|268611153|ref|ZP_06144880.1| 23.36 441 286 7 543 1856 547 938 4e-31 141 +phage_suis gi|268611153|ref|ZP_06144880.1| 25.27 459 266 11 522 1844 722 1121 8e-31 140 +phage_suis gi|268611153|ref|ZP_06144880.1| 24.63 406 267 8 501 1694 770 1144 3e-23 115 +phage_suis gi|268611153|ref|ZP_06144880.1| 27.80 241 145 3 492 1148 811 1044 6e-16 90.9 +phage_suis gi|268611153|ref|ZP_06144880.1| 19.76 253 168 6 1158 1883 547 775 3e-04 52.0 +phage_suis gi|268610688|ref|ZP_06144415.1| 28.95 639 369 11 78 1847 440 1042 3e-59 234 +phage_suis gi|268610688|ref|ZP_06144415.1| 24.64 491 316 9 501 1856 770 1245 4e-39 167 +phage_suis gi|268610688|ref|ZP_06144415.1| 23.79 517 319 9 492 1832 811 1322 3e-37 161 +phage_suis gi|268610688|ref|ZP_06144415.1| 21.91 493 322 11 510 1859 905 1377 1e-25 123 +phage_suis gi|268610688|ref|ZP_06144415.1| 20.55 292 197 5 486 1343 1138 1400 4e-10 71.6 +phage_suis gi|268610688|ref|ZP_06144415.1| 21.41 341 225 10 894 1883 467 775 8e-05 53.9 +phage_suis gi|153811333|ref|ZP_01964001.1| 28.34 621 364 16 108 1847 493 1073 8e-55 219 +phage_suis gi|153811333|ref|ZP_01964001.1| 29.67 428 250 9 519 1760 709 1099 2e-47 195 +phage_suis gi|153811333|ref|ZP_01964001.1| 29.41 391 226 7 498 1640 746 1096 1e-39 169 +phage_suis gi|153811333|ref|ZP_01964001.1| 26.49 268 174 3 492 1256 854 1111 3e-24 118 +phage_suis gi|153811333|ref|ZP_01964001.1| 27.12 306 198 4 510 1385 816 1110 1e-23 116 +phage_suis gi|262113750|emb|CAR95417.1| 38.46 286 169 1 384 1241 540 818 2e-54 218 +phage_suis gi|262113750|emb|CAR95417.1| 29.68 411 271 7 657 1871 460 858 3e-40 171 +phage_suis gi|77411259|ref|ZP_00787609.1| 37.19 285 172 1 387 1241 628 905 2e-53 215 +phage_suis gi|77411259|ref|ZP_00787609.1| 28.01 407 281 6 660 1871 548 945 1e-40 172 +phage_suis gi|77411259|ref|ZP_00787609.1| 22.82 355 207 7 978 1877 540 882 9e-14 83.6 +phage_suis gi|76786754|ref|YP_329383.1| 36.84 285 173 1 387 1241 628 905 8e-53 213 +phage_suis gi|76786754|ref|YP_329383.1| 27.27 407 284 6 660 1871 548 945 3e-38 164 +phage_suis gi|76786754|ref|YP_329383.1| 24.73 283 194 2 543 1391 637 900 3e-23 115 +phage_suis gi|76786754|ref|YP_329383.1| 22.91 323 204 6 978 1847 540 850 2e-13 82.4 +phage_suis gi|50914476|ref|YP_060448.1| 35.86 290 179 1 372 1241 623 905 4e-51 207 +phage_suis gi|50914476|ref|YP_060448.1| 27.01 411 280 7 660 1871 548 945 2e-35 155 +phage_suis gi|50914476|ref|YP_060448.1| 23.00 387 269 5 543 1673 637 1004 3e-25 121 diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003.smp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd00003.smp Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,19957 @@ +PssmWithParameters ::= { + pssm { + isProtein TRUE, + numRows 28, + numColumns 234, + byRow FALSE, + query seq { + id { + general { + db "CDD", + tag id 237977 + } + }, + descr { + title "cd00003, PNPsynthase, Pyridoxine 5'-phosphate (PNP) synthase + domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as + an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, + formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin + B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP + biosynthesis, the condensation of 1-amino-acetone 3-phosphate and + 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology, + intersubunit contacts are mediated by three ''extra'' helices, generating a + tetramer of symmetric dimers with shared active sites; the open state has + been proposed to accept substrates and to release products, while most of the + catalytic events are likely to occur in the closed state; a hydrophilic + channel running through the center of the barrel was identified as the + essential structural feature that enables PNP synthase to release water + molecules produced during the reaction from the closed, solvent-shielded + active site." + }, + inst { + repr raw, + mol aa, + length 234, + seq-data ncbieaa "RLGVNIDHVATLRNARGTNYPDPVEAALLAEKAGADGITVHLREDRRHIQDR +DVRLLRELVRTELNLEMAPTEEMLEIALEVKPHQVTLVPEKREELTTEGGLDVAGQAEKLKPIIERLKDAGIRVSLFI +DPDPEQIEAAKEVGADRVELHTGPYANAYDKAEREAELERIAKAAKLARELGLGVNAGHGLNYENVKPIAKIPGIAEL +NIGHAIISRALFVGLEEAVREMKDLI" + } + }, + intermediateData { + weightedResFreqsPerPos { + { 0, 10, 0 }, + { 575880368388257, 10, 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-594, + -334, + -636, + -593, + 485, + -545, + 343, + 529, + -604, + -586, + -513, + -556, + -479, + -56, + 41, + -533, + -100, + -450, + -32768, + -32768, + -400, + -32768, + -32768 + }, + lambda { 267, 10, -3 }, + kappa { 695502437462053, 10, -16 }, + h { 14, 10, -2 }, + scalingFactor 100, + lambdaUngapped { 315181590957692, 10, -15 }, + kappaUngapped { 22723615854819, 10, -14 }, + hUngapped { 852942415611443, 10, -15 } + } + }, + params { + pseudocount 10, + rpsdbparams { + matrixName "BLOSUM62" + } + } +} diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.aux --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd00003_and_cd00008.aux Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,12 @@ +BLOSUM62 +11 +1 +0.000000e+00 +0.000000e+00 +0 +0 +100.000000 +234 +6.955024e-02 +160 +4.862535e-02 diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.freq Binary file test-data/cd00003_and_cd00008.freq has changed diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.loo Binary file test-data/cd00003_and_cd00008.loo has changed diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.phr Binary file test-data/cd00003_and_cd00008.phr has changed diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.pin Binary file test-data/cd00003_and_cd00008.pin has changed diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.psd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd00003_and_cd00008.psd Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,2 @@ +gnl|cdd|1890191 +gnl|cdd|2379770 diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.psi Binary file test-data/cd00003_and_cd00008.psi has changed diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.psq Binary file test-data/cd00003_and_cd00008.psq has changed diff -r 000000000000 -r 432ea9614cc9 test-data/cd00003_and_cd00008.rps Binary file test-data/cd00003_and_cd00008.rps has changed diff -r 000000000000 -r 432ea9614cc9 test-data/cd00008.smp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cd00008.smp Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,13679 @@ +PssmWithParameters ::= { + pssm { + isProtein TRUE, + numRows 28, + numColumns 160, + byRow FALSE, + query seq { + id { + general { + db "CDD", + tag id 189019 + } + }, + descr { + title "cd00008, PIN_53EXO-like, PIN domains of the 5'-3' exonucleases + of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and + homologs. PIN (PilT N terminus) domains of the 5'-3' exonucleases (53EXO) of + mutli-domain DNA polymerase I and single domain protein homologs, as well as, + the PIN domains of bacteriophage T5-5'nuclease (T5FEN or 5'-3'exonuclease), + bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage + exodeoxyribonuclease) and other similar nucleases are included in this + family. The 53EXO of DNA polymerase I recognizes and endonucleolytically + cleaves a structure-specific DNA substrate that has a bifurcated downstream + duplex and an upstream template-primer duplex that overlaps the downstream + duplex by 1 bp. The T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also + exhibits endonucleolytic activity on flap structures (branched duplex DNA + containing a free single-stranded 5'end). T4 RNase H, which removes the RNA + primers that initiate lagging strand fragments, has 5'- 3'exonuclease + activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on + flap or forked DNA structures. These nucleases are members of the + structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA + duplex-containing nucleic acid structures during DNA replication, repair, and + recombination. They contain a PIN domain with a helical arch/clamp region (I + domain) of variable length (approximately 16 to 30 residues in 53EXO-like PIN + domains) and a H3TH (helix-3-turn-helix) domain, an atypical + helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) + and the helical arch/clamp region are involved in DNA binding. The active + site of the 53EXO of Taq DNA polymerase I includes a set of conserved acidic + residues that are essential for binding three divalent metal ions (two Mn2+ + ions and one Zn2+ ion) required for nuclease activity. T5-5'nuclease requires + at least two bound divalent metal ions for nuclease activity and is reported + to be able to use Mg2+, Mn2+ or Co2+ as co-factors." + }, + inst { + repr raw, + mol aa, + length 160, + seq-data ncbieaa "LMLVDGTNLAFRTKHNNSKKKEKINLSPFASSYVSSIQSLAKSYSARTTIVL +GDKGKSVFRLEHLPEYKGNRDEKYAEEKALDEQFFEYLKDAFELCKATTFPTFTIRGYEADDMAAYLVKKIGHEGDHV +WIISTDGDWDQLLTDKVSRFSPTTRREYHL" + } + }, + intermediateData { + weightedResFreqsPerPos { + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 338020833333333, 10, -15 }, + { 0, 10, 0 }, + { 328645833333333, 10, -15 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 333333333333333, 10, -15 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 0, 10, 0 }, + { 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-32768, + -136, + -32768, + -287, + -161, + -56, + -281, + -243, + 591, + -274, + 318, + -281, + -184, + -43, + -206, + -7, + 7, + -29, + 308, + -222, + -337, + -100, + -69, + -32768, + -32768, + -399, + -32768, + -32768, + -32768, + -187, + -32768, + -240, + -339, + -301, + -129, + -391, + -351, + 323, + -269, + 251, + 24, + -362, + 495, + -275, + -318, + -249, + -165, + 48, + -331, + -100, + -238, + -32768, + -32768, + -399, + -32768, + -32768 + }, + lambda { 267, 10, -3 }, + kappa { 486253485452101, 10, -16 }, + h { 14, 10, -2 }, + scalingFactor 100, + lambdaUngapped { 318588052238909, 10, -15 }, + kappaUngapped { 158869858915243, 10, -15 }, + hUngapped { 43477934178065, 10, -14 } + } + }, + params { + pseudocount 10, + rpsdbparams { + matrixName "BLOSUM62" + } + } +} diff -r 000000000000 -r 432ea9614cc9 test-data/chimera.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimera.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,168 @@ +>chimera chunks of AB011145 plus M10051 plus BC112106 +GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC +CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC +TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT +TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA +CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA +CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC +TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA +TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG +GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA +TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA +ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA +CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC +AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT +CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC +CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA +TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG +CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC +CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA +GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT +ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA +GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT +CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT +GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA +TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA +CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA +AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG +GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG +AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT +TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT +TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT +TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG +CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA +CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT +TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC +TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT +GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT +AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT +TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT +GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT +TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA +GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA +TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA +TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT +AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT +TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT +ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT +GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA +GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT +GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT +TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT +TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT +AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG +AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC +TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT +CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA +GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT +TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT +GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT +TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG +GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA +CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA +CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA +GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA +GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT +GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG +GAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCA +ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA +AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA +ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA +GGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGAT +TGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGA +CCCCGCGCTCCCGCAGCCATGGGCACCGGGGGCCGGCGGGGGGCGGCGGCCGCGCCGCTG +CTGGTGGCGGTGGCCGCGCTGCTACTGGGCGCCGCGGGCCACCTGTACCCCGGAGAGGTG +TGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCT +GTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGA +GACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTAT +GGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTG +TTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTAC +AACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTAC +TTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTG +AACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACC +AACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCAC +TGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGT +TGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCC +TGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCAC +TTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAG +AACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAG +TGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCC +TGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCC +CAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGC +AACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTAT +CTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTG +ATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAAC +CTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTC +TTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGA +ACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCC +TGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTG +AGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTAC +AAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAAC +AGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAAC +CACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAG +ACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTAT +GTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCA +TCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCAC +TACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGC +CTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT +CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG +ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT +TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC +CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG +CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG +CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC +TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC +AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT +GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG +AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG +GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT +GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC +TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT +GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT +ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT +TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC +GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC +GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG +GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG +GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC +AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC +CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA +GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG +TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA +ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC +AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC +ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA +CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT +CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA +TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG +CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT +GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC +TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC +TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG +ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT +CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT +CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG +GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC +TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT +CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC +ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT +TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG +GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC +CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA +CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC +TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC +TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG +GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC +CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG +GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA +GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG +CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT +GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG +CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA +GCCATCCCACCAG diff -r 000000000000 -r 432ea9614cc9 test-data/convert2blastmask_four_human_masked.maskinfo-asn1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/convert2blastmask_four_human_masked.maskinfo-asn1 Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,158 @@ +Blast-db-mask-info ::= { + algo-id 0, + algo-program seg, + algo-options "window=12; locut=2.2; hicut=2.5", + masks { + masks { + int { + from 6, + to 18, + id swissprot { + name "ERP44_HUMAN", + accession "Q9BS26", + release "reviewed" + } + }, + packed-int { + { + from 11, + to 46, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 325, + to 332, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 421, + to 496, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 501, + to 516, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 536, + to 558, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 636, + to 648, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 737, + to 762, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 789, + to 806, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 970, + to 983, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + }, + { + from 999, + to 1010, + id swissprot { + name "BMP2K_HUMAN", + accession "Q9NSY1", + release "reviewed" + } + } + }, + packed-int { + { + from 3, + to 26, + id swissprot { + name "INSR_HUMAN", + accession "P06213", + release "reviewed" + } + }, + { + from 372, + to 390, + id swissprot { + name "INSR_HUMAN", + accession "P06213", + release "reviewed" + } + }, + { + from 766, + to 791, + id swissprot { + name "INSR_HUMAN", + accession "P06213", + release "reviewed" + } + }, + { + from 1312, + to 1324, + id swissprot { + name "INSR_HUMAN", + accession "P06213", + release "reviewed" + } + } + }, + int { + from 230, + to 246, + id swissprot { + name "OPSD_HUMAN", + accession "P08100", + release "reviewed" + } + } + }, + more FALSE + } +} diff -r 000000000000 -r 432ea9614cc9 test-data/convert2blastmask_four_human_masked.maskinfo-asn1-binary Binary file test-data/convert2blastmask_four_human_masked.maskinfo-asn1-binary has changed diff -r 000000000000 -r 432ea9614cc9 test-data/dustmasker_three_human.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,183 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG +CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC +GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC +CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC +TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT +TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA +CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA +CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC +TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA +TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG +GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA +TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA +ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA +CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC +AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT +CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC +CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA +TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG +CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTatttttattttgaataaacagaaagaaattttgggtttttaatttttttCTCC +CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTaaaaaaaaaaaaaCCTGCTA +GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT +ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA +GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT +CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT +GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA +TTGCTTATGAAAATTCCATAGTGGTAtttttttGGATTCTTAATGTGTAACTTAAACATA +CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA +AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG +GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG +AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT +TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT +TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACtt +tttttCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG +CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA +CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT +TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC +TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT +GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT +AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT +TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT +GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT +TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA +GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA +TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA +TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT +AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT +TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT +ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT +GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA +GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT +GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT +TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT +TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT +AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG +AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC +TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT +CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA +GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT +TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT +GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT +TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG +GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA +CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA +CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA +GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA +GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT +GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG +GAAACTTTTAGATGACATTCTACAAATTAtttttttCTTTAAATTAAAAGAACCTAGCCA +ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA +AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA +ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA +GGTTGTCAAGAAGGCttttttttttttcttttttAAACCTGAGGGCAAAAAGGAATGGAT +AAAGTAGTGTAATGGATTGACAATCAGGAAGAACAGAATAACTCAGtttttttttCTCCT +ACAAGGAGATATGGCTGGACCAAAATAAAATGACATGAAATTGCAAAAATGAAAAT +>ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds +GGGGGGCTGCGCGGCCGGGTCGGTGCGCACACGAGAAGGACGCGCGGCCCCCAGCGCTCT +TGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGA +CCCCGCGCTCCCGCAGCCAtgggcaccgggggccggcggggggcggcggccgcgccgctg +ctggtggcggtggccgcgctgctactgggcgccgcgggccACCTGTACCCCGGAGAGGTG +TGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCT +GTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGA +GACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTAT +GGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTG +TTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTAC +AACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTAC +TTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTG +AACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACC +AACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCAC +TGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGT +TGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCC +TGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCAC +TTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAG +AACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAG +TGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCC +TGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCC +CAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGC +AACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTAT +CTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTG +ATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAAC +CTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTC +TTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGA +ACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCC +TGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTG +AGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTAC +AAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAAC +AGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAAC +CACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAG +ACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTAT +GTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCA +TCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCAC +TACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGC +CTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT +CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG +ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT +TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC +CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG +CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG +CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC +TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC +AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT +GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG +AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG +GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT +GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC +TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT +GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT +ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT +TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC +GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC +GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG +GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG +GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC +AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC +CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA +GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG +TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA +ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC +AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC +ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA +CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT +CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA +TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG +CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT +GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC +TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC +TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG +ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT +CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT +ACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGAC +TCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAA +GGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGT +TTTTTCGTTccccccacccgcccccAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATT +CttttttttttttttttttttttttttttGCTGGTGTCTGAGCTTCAGTATAAAAGACAA +AACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA +>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds +CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGC +CACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTG +CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG +GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC +TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT +CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC +ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT +TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG +GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC +CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA +CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC +TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC +TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG +GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC +CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG +GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA +GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG +CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT +GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG +CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA +GCCATCCCACCAG diff -r 000000000000 -r 432ea9614cc9 test-data/dustmasker_three_human.maskinfo-asn1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.maskinfo-asn1 Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,64 @@ +Blast-db-mask-info ::= { + algo-id 2, + algo-program dust, + algo-options "window=64; level=20; linker=1", + masks { + masks { + packed-int { + { + from 1447, + to 1495, + id local id 1 + }, + { + from 1540, + to 1552, + id local id 1 + }, + { + from 1886, + to 1892, + id local id 1 + }, + { + from 2278, + to 2284, + id local id 1 + }, + { + from 4409, + to 4415, + id local id 1 + }, + { + from 4635, + to 4653, + id local id 1 + }, + { + from 4726, + to 4734, + id local id 1 + } + }, + packed-int { + { + from 139, + to 219, + id local id 2 + }, + { + from 4569, + to 4584, + id local id 2 + }, + { + from 4621, + to 4648, + id local id 2 + } + } + }, + more FALSE + } +} diff -r 000000000000 -r 432ea9614cc9 test-data/dustmasker_three_human.maskinfo-asn1-binary Binary file test-data/dustmasker_three_human.maskinfo-asn1-binary has changed diff -r 000000000000 -r 432ea9614cc9 test-data/empty_file.dat diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.dbinfo.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.dbinfo.txt Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,7 @@ +Database: Just 4 human proteins + 4 sequences; 3,297 total residues + +Date: Feb 10, 2014 6:40 PM Longest sequence: 1,382 residues + +Volumes: + /mnt/galaxy/galaxy_blast/test-data/four_human_proteins_taxid.fasta diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,48 @@ +>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 +MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFP +NENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSK +RNIIGYFEQKDSDNYRVFERVANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHADCDKFRHPLLHIQKTPADCPV +IAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREFHHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLL +RDRDEL +>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 +MKKFSRMPKSEGGSGGGAAGGGAGGAGAGAGCGSGGSSVGVRVFAVGRHQVTLEESLAEGGFSTVFLVRTHGGIRCALKR +MYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSISDNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFC +DTCEAVARLHQCKTPIIHRDLKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEPDPEHRPDIFQVSYFAFKFAK +KDCPVSNINNSSIPSALPEPMTASEAAARKSQIKARITDTIGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLA +PGEFGNHRPKGALRPGNGPEILLGQGPPQQPPQQHRVLQQLQQGDWRLQQLHLQHRHPHQQQQQQQQQQQQQQQQQQQQQ +QQQQQQHHHHHHHHLLQDAYMQQYQHATQQQQMLQQQFLMHSVYQPQPSASQYPTMMPQYQQAFFQQQMLAQHQPSQQQA +SPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSVADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTEEEL +LDREFDLLRSNRLEERASSDKNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNDESESDFESDPPSPKSSEEEEQDDEEVLQGEQGDFNDDDTEPENLGHRPLLMDSEDEEEEEKH +SSDSDYEQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSAQLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNL +PQHRFPAAGLEQEEFDVFTKAPFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVKQRSLQKLSSRQRRTKQDMSKSNGKRHHGTPTSTKKTLKPTYRTPERARRHKKVGRRDSQSSNEFLTISD +SKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLSWHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKM +DDFGAVPFTELVVQSITPHQSQQSQPVELDPFGAAPFPSKQ +>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 +MATGGRRGAAAAPLLVAVAALLLGAAGHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHLQILLMFKTRPEDFRDLSFPK +LIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYALVIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDW +SRILDSVEDNYIVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQGCHQYVIHNNKCIPECPSGYT +MNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGCTVINGSLIINIRGGNNLAAELEANLGLIEEISGYLKIRRS +YALVSLSFFRKLRLIRGETLEIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE +RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQNVTEFDGQDACGSNSWTVVD +IDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFSDERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIIL +KWKPPSDPNGNITHYLVFWERQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL +KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDVGNVTVAVPTVAAFPNTSSTSVPTSPEEHRPFEK +VVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYVSARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGL +IVLYEVSYRRYGDEELHLCVSRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG +PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSREKITLLRELGQGSFGMVYEG +NARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRP +EAENNPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV +RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMR +PTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPESEELEMEFEDMENVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIP +YTHMNGGKKNGRILTLPRSNPS +>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFT +WVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES +ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTT +ICCGKNPLGDDEASATVSKTETSQVAPA diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta.log.txt Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,5 @@ +New DB title: Just 4 human proteins +Sequence type: Protein +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.phd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta.phd Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,4 @@ +11117184492 +29249033410 +36665887501 +5392473183 diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.phi Binary file test-data/four_human_proteins.fasta.phi has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.phr Binary file test-data/four_human_proteins.fasta.phr has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.pin Binary file test-data/four_human_proteins.fasta.pin has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.pog Binary file test-data/four_human_proteins.fasta.pog has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.psd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins.fasta.psd Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,4 @@ +gnl|bl_ord_id|00 +gnl|bl_ord_id|11 +gnl|bl_ord_id|22 +gnl|bl_ord_id|33 diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.psi Binary file test-data/four_human_proteins.fasta.psi has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins.fasta.psq Binary file test-data/four_human_proteins.fasta.psq has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_masked.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins_masked.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,61 @@ +>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 +MHPAVFlslpdlrcsllllVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF +SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK +REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER +VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD +CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF +HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL +>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 +MKKFSRMPKSEggsgggaagggaggagagagcgsggssvgvrvfavgRHQVTLEESLAEG +GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS +DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD +LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP +DPEHRPDIFQVSYFAFKFAKKDCPVsninnssiPSALPEPMTASEAAARKSQIKARITDT +IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE +Illgqgppqqppqqhrvlqqlqqgdwrlqqlhlqhrhphqqqqqqqqqqqqqqqqqqqqq +qqqqqqhhhhhhhhllqDAYMqqyqhatqqqqmlqqqFLMHSVYQPQPSASQYPTMmpqy +qqaffqqqmlaqhqpsqqqASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV +ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTeeelldrefdllrSNRLEERASSD +KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNdesesdfesdppspksseeeeqddeeVLQGEQGDFNDDDTEPE +NLGHRPLLMdsedeeeeekhssdsdyeQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA +QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK +APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVkqrslqklssrqrrTKQDMSKSNGKRHHGtptstkktlkptYRTPERARR +HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS +WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ +SQQSQPVELDPFGAAPFPSKQ +>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 +MATggrrgaaaapllvavaalllgaagHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL +QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL +VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE +ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG +CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC +TVINGSLIINIRggnnlaaeleanlglieeiSGYLKIRRSYALVSLSFFRKLRLIRGETL +EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE +RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ +NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS +DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE +RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL +KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDvgnvtvavptvaaf +pntsstsvptspEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV +SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV +SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG +PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR +EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG +FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA +AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV +RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN +CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPeseeleme +fedmeNVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN +PS +>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY +VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG +GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP +EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVkeaaaqqqes +attqkaeKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI +YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins_taxid.fasta.log.txt Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,5 @@ +New DB title: Just 4 human proteins +Sequence type: Protein +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.phd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins_taxid.fasta.phd Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,4 @@ +11117184492 +29249033410 +36665887501 +5392473183 diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.phi Binary file test-data/four_human_proteins_taxid.fasta.phi has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.phr Binary file test-data/four_human_proteins_taxid.fasta.phr has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.pin Binary file test-data/four_human_proteins_taxid.fasta.pin has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.pog Binary file test-data/four_human_proteins_taxid.fasta.pog has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.psd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/four_human_proteins_taxid.fasta.psd Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,4 @@ +gnl|bl_ord_id|00 +gnl|bl_ord_id|11 +gnl|bl_ord_id|22 +gnl|bl_ord_id|33 diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.psi Binary file test-data/four_human_proteins_taxid.fasta.psi has changed diff -r 000000000000 -r 432ea9614cc9 test-data/four_human_proteins_taxid.fasta.psq Binary file test-data/four_human_proteins_taxid.fasta.psq has changed diff -r 000000000000 -r 432ea9614cc9 test-data/rhodopsin_nucs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rhodopsin_nucs.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,161 @@ +>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA +ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCT +TCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCT +CATCGTGCTTGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACG +CCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCA +CCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGC +CACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTGAGCGGTACGTGGTGGTGTGT +AAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACCTGGGTCATGG +CACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATG +CGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTC +CACTTCACCATCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGG +CAGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCAT +GGTCATTGCTTTCCTGATCTGTTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGG +TCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCTTCGCAAAGTCCTCCTCCATCTACAACCCTG +TCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCC +ACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACCGGCCTAA + +>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds +TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCCAAACTTTTA +CATACCCATGTCCAACAAGACTGGGGTGGTGCGAAGCCCCTTTGAATACCCTCAGTATTACCTGGCAGAG +CCATGGCAATATTCCATTCTGTGCGCGTACATGTTCCTGCTCATTCTACTTGGGTTCCCAATCAACTTCA +TGACCTTGTACGTCACCATCCAGCACAAGAAGCTCCGGACACCCTTAAACTATATCCTGCTGAATTTGGC +CTTTGCCAACCACTTCATGGTCCTGTGTGGATTCACGGTGACAATGTACTCCTCAATGAACGGATACTTC +ATCCTCGGAGCCACCGGTTGCTATGTTGAAGGCTTCTTCGCTACCCTTGGTGGTGAAATCGCCCTTTGGT +CCCTGGTGGTCTTGGCCATTGAACGATACGTGGTCGTCTGTAAGCCCATGAGCAACTTCCGATTTAGTGA +GAACCATGCCGTCATGGGCGTAGCGTTCACCTGGATAATGGCTTTGTCCTGTGCTGTTCCTCCACTCCTT +GGATGGTCCAGGTACATCCCCGAGGGCATGCAGTGCTCCTGCGGAGTCGACTACTACACCCTGAAGCCCG +AGGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTCGTCCACTTCACCATCCCCCTGATTATCATTTT +CTTCTGCTATGGCCGCCTGGTGTGCACTGTGAAAGAGGCTGCAGCTCAACAGCAAGAGTCCGCCACCACC +CAGAAGGCCGAGAAAGAGGTGACCAGGATGGTGATCATCATGGTGGTCTTCTTCCTTATCTGTTGGGTCC +CCTACGCCTCTGTCGCTTTCTTCATCTTCAGCAATCAGGGCTCTGAGTTCGGCCCCATCTTCATGACCGT +CCCAGCTTTCTTTGCCAAGAGTTCTTCCATCTACAACCCCGTCATCTACATCATGCTCAACAAGCAGTTC +CGTAACTGCATGATCACCACCCTGTGCTGCGGCAAGAATCCCTTTGGAGAAGACGATGCCTCCTCTGCCG +CCACCTCCAAGACAGAGGCTTCTTCTGTTTCTTCCAGCCAGGTGTCTCCTGCATAAGACCTTCCACCAGG +CCTGTCTCAGGGTCCGCTGCCTCACACAGCTCCCACCGCCCCAACTCCGTCTCCTGCTCGCTAAGGCGGC +GAAGTTCCCCTTCCATTACATAAAACGTATCTGTTCAAGAAAGGCGACGACGAAGGAGAAGAAGAGGAGC +CCCCCCGAACCCCTTCGCTGCTGCTGAAAACGACTTGATTGCTTCTGCAACGCAACGGGGCCTTACGGCA +GCGAAGGGGTTGTCATCCGGACGCGCCAAGAATTCCTTCGAGACTGTAAATATCTTAAAGGAACCGTCCT +GCTAGTTACCGACGCCGCTCCTGTAGCCGCCGTTCCCCCGCACTCCGGCCGGTTCATACCTCTTATTTTT +TTGCAATGCAACAGAAAATAATATTTTTGTTCCCACGGCTTTTCCCGGTCAGGTCTGGTAGTGGCGGAGA +TTGGCCGACCCCTCGCACCTGTAATAAAGCGCAG + +>gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds +GTGCCCTTCTCCAACAAGACAGGCGTGGTGCGCAGTCCCTTCGAGCATCCACAGTACTACCTGGCCGAGC +CATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTCGGCTTCCCCATCAACTTCCT +CACGCTCTATGTCACGGTTCAGCACAAGAAGCTGCGTACGCCTCTCAACTACATCCTGCTCAACCTGGCC +GTGGCCGACCTCTTCATGGTCTTCGGAGGCTTCACCACCACCCTCTACACCTCCCTGCATGGATACTTTG +TCTTCGGGCCTACGGGATGCAATCTGGAGGGCTTTTTTGCCACCCTGGGAGGTATGAGCTGAGATGCGGG +TAAGGAGGAGGCATAGAGGCATCTGGGAACAGTCCCAAGCTTGGGGTGAAGGCTAAGAGGCCTTCTTCCT +TGTTCTGTCATTGGCGTCGTCCGAAGCCCTCACTTAATCAACAAACAGTTTGGTGGTGAGGCGCTGAGCT +CCATTTGGAGAGGGCAGGTATCGAGCACTGTTTTATCCCCCCTGGAGTGGTGCCATTGCCTTGCTTTACA +GCAAAGAAACTGAGGATGAGAGGAGTCGAGGGTCTTGCCAGGTCACATCATGGCAGAGACAGAGCTGAGT +TTCAACCCTGCATCTATGTGCAGTTTCCCTTGGAGCAGCTATGTTAGGTCAGACCCACGGTGGGCACTGG +GGAGAGAGCTGCACAAGACAGGTCCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTCCTGATTGCCA +GGAGTGATGTGCAGCGCAAATGTCTGAATTCCATTATTATGTGCTCCTTCTTCCTCTGAGCCAAACATCC +ATCTTCATGGCTCCTAGAATTGGGTCCCACCCACATGAGCAGGTCATTTTGTTTCCCTAGAGGGGAGAGG +TCACTGCTGTGGAGGGAGGGAAGGTTCGTCCCGCTCCATGTTTCTGTTGTCTCTGCAATGCCTTTCTCTA +GGGACTCTGCCTATTGCCCCAAGAAGGACACATTCTTCTGTAAAAACTCCCTCCTGGGTTCCCAGTCTAA +TCAAGACCTCTAAACTGATTTCCATGTCCCTCATGAACCCAAAGCTCTAACTGAATTAAACTTCTCAGGA +CTTACTCCACTCTCCTCGTCCATCATGCAGCCCCTCTGCCCAGCACCCTATCTCCTCTTCTTCCCAGTGT +CTGAGCCCACTGTACCCTGAGACTTCGCTCCAGGCCTGCCCCAGGCTGCCTTCTCAGGTGCCCTCTCCCA +CATAGGAGGAGCACGGCCTCCTTAGACAGACGTGGGGTGCAGGTTGGTGGCATGCTGACTGATAGCTGAC +TGCCTTGCAGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTATGCA +AGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCCTTGCCCTCACCTGGGTCATGGC +ACTGGCCTGCGCCGCGCCCCCGCTAGTCGGCTGGTCCAGGTAATGGCACTGAACAGAAGGGAAGTGCCTC +TGAGGTCTTCTTAGGGTCCCCCAGCTGGGACTCAAACCTAGGGCTGTCTGGTTCCAGGCACGGAACTGGC +GACTCCACTGGGGTTGGGGTTTAGGGCAAGGAAGGAGAGGATCAGACCCTAATGTTGTTACGTGGGTTGG +TCCGCATGTCAAGGAGAATCCAAGACACCCAATCCTTCACCTTGGCTGTGCCCCTAATCCTCATCTAAGC +CAGGTTCAGATTCCAATCCTCTTTGGCCCAGTGCTCCGTGGGAAGCTCCCTCTGACCTTGGGCCTCAGCG +CCTGGGGTTGCTGAGCCTTCCTAGTATAGGTGGTGACATCGTAGCCCCTGGGACCTGGATCCTGCCCAGT +CTGCAGGCCATCATCTCCAAATGGGGCTGAGATGAGATGTGAGGAAAGAGGGGAGACAGTGGTTTGGAAA +ACTGGACTGGTGGCTTTTTTGGGTTTCCAGAGGACTCATCTTCCTCTGCTTCTAGAATATTCCCACTCTC +TCTTCCCTTTCCTCATTCTTCCTGGGTTATTTTTTTTTCCCTTTGCTGAATTCGAGCCCCATTCCCTCCA +GCCTCTTTCCCTGTCTTATCTAGCCCAGTCCAGTTATATTCTCATAGGCAGAGGCAACAGATGCTCCAAA +TTTTCTGAGGTCGGTTCCAACATCGCCACCCTCTAAAATCAGTGAAACATCCTAACTACATGCCTCATAG +TCCTCCTGTTTCCAAAAACTGCAAAGATCTCCTGGTTACCCTGTATGCCCATCTTTGGGCTAGAAAATCC +TCTCACCCTGTTAATAGTAAGACCCTGGTTTGTACAAACTGCCTCAAACACAGAGTTTAGGGGCTTTTCC +CTTCTCTCCGCCAACCTCTGACAGGCAGAGTCTGAGGCCTGGCCTCCAGCTGCTGCGGGGAGCAGGTCTG +GTAAAGAATCCTGTGCAGGTCAGTGGTATACAGGTCCTGTCAGGTGACAGCCTGGGCGAGAGACTGGAAA +GTATCAGGATAACACGGCTGCCAGACGAACAACAAAACAACACTGAATTCACAAGGCGCATTCGAATCCT +CTCTCAGTCCATTTGATCCTCAGTCACACAGCCGAGTAGACACTTTATCAACTCATTTAACAGAAAGGGA +AAGTGAAGCCCAGAGCGAGGCCAGCAACGTGGCAGGTCACTCTGGTCATCTAGGGCCTGTTCCCAACTCT +TTCACATGTGGGTCTCCAATATGTTCCCTCCTGTCCCAATCTCTGCCGGCCCTCAGGTACATCCCAGAGG +GCATGCAGTGCTCATGTGGAATCGACTACTACACCCTCAAGCCGGAGGTCAACAACGAGTCCTTTGTCAT +CTACATGTTCGTGGTCCACTTCACCATCCCTATGATTGTCATATTCTTTTGCTATGGACAGCTGGTCTTC +ACCGTCAAGGAGGTAAGGTCATGTGTTGGGCACTGGGGACATGCACACTGAGTGAATGGAGCCCAGCTCC +ATTCCCAGAGTTGCCACAGTCTGGACACCTGACCTTGTGTCCCTGCAGGCAGCTGCCCAGCAGCAGGAGT +CAGCCACCACCCAGAAGGCCGAGAAGGAGGTCACCCGTATGGTCATCATCATGGTCATTGCTTTCCTAAT +CTGTTGGCTGCCGTATGCCGGCGTGGCATTCTACATCTTCACCCACCAGGGCTCTAACTTTGGCCCCATC +TTCATGACCCTCCCGGCATTCTTTGCCAAGTCGTCCTCCATCTACAACCCTGTCATCTATATCATGATGA +ACAAGCAGGTGCCAGGTGGTAGGGAGGGAGGGTCTGGGTCCCCCAGGCTGCAGGCACTGCCCACAGAGGA +CAAGCCACATCCTTGACTAGGCAGACCCCAGTCTTCCCATCTGCAAAATTAGGCAGGGGAGTTCGTCTCC +CCCAGGCATCAGAGACATCGGGGAGAAATGCACATTTCTGGAGATGAATCAGCATCTCAGGGTGGGCCCA +GGAACCTGCACTTCTAAAAACCATTCCACATGACTCTGAGGCTAGCATGAGAAGTGATGATCCACATGGT +TCTGGAGGCCTGCTTTAAAAGTCAAGTGGTCAAAGTCCCAAGCCTGGGAACGGGATGGTGCCAGTCTCCA +TTAAAGAGATCAAAAGGAGCTAGAAAGTCTTGTGATGAAAGATGAAGGGATAAAGCCGTCCTTTAACACA +GATCAGTGATTTCTCTGCAGAATCCATGACCCAGTGGGAAAAAGTGGTCCCTGGAGTCAGGCATATTGGA +TTCAAATCCTAGCTCTGCTATTTTCTAGCTATGTAACCTTGGGCAAGTCATCTCCCTTCTCTGTGCTTCA +GTTTCTTCTTTCATAGAAAGGGTAAAATCCCAAACTCTTGGGTTAAATGAGATAACTTACATAGCCCTTG +ATATGCAGAGGCATTATGGAATGTCGTTAGTGACAAAGTTCCCTTGGGTTTGGTCCCTGGTATCTCTGGA +GTGAGATTGCATATGTTCCCTTCAGAGGGTCAGATTTGGGATGAGAGTGGAGGCTGCGAGGGCCTGAGTG +GGAAGGGATTGGAGGCAAATCTCACCAACCATGTCAGTTTGCTACACACACTTTGGGTGGACCCTGACCC +TGACTCATGCTTCTTGCCTTCCAGTTCCGGAACTGCATGCTCACTACCCTCTGCTGTGGCAAGAACCCAC +TGGGTGACGATGAGGCCTCCACCACTGCCTC + +>gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds +GTGCCCTTCTCCAACAAGACGGGTGTGGTGCGCAGCCCCTTCGAGTACCCGCAGTACTACCTGGCTGAGC +CCTGGCAGTTCTCCATGCTGGCTGCCTACATGTTTCTGCTGATCGTGCTCGGATTCCCCATCAACTTCCT +CACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCT +GTGGCCAACCTCTTCATGGTCTTTGGAGGCTTCACCACCACCCTGTATACCTCTATGCATGGATACTTCG +TCTTCGGGGCCACGGGATGCAATCTGGAGGGCTTCTTTGCCACGCTGGGCGGTGAAATCGCCCTGTGGTC +CCTGGTGGTCCTGGCCATCGAGCGGTATGTGGTGGTCTGCAAGCCCATGAGCAACTTCCGCTTTGGGGAG +AACCACGCCATCATGGGCCTCGCCTTCACGTGGGTCATGGCACTGGCCTGCGCTGCACCCCCACTAGCCG +GCTGGTCCAGGTACATCCCAGAGGGCATGCAGTGCTCGTGTGGGATTGACTACTACACGCTCAAACCGGA +GGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTGTCATTTTC +TTCTGCTACGGACAGCTGGTGTTCACAGTGAAGGAGGCGGCTGCCCAGCAGCAGGAGTCAGCCACCACCC +AGAAGGCCGAGAAGGAAGTCACGCGCATGGTCATCATCATGGTCGTTGCGTTCCTAATCTGTTGGCTGCC +CTACGCCAGCGTGGCATTCTACATCTTTACCCACCAGGGCTCTAACTTTGGCCCTGTCTTCATGACCATC +CCGGCATTCTTCGCCAAGTCATCCTCCATCTACAACCCGGTCATCTATATCATGATGAACAAGCAGTTCC +GGAACTGCATGCTCACCACCCTCTGCTGTGGCAAGAACCCACTGGGTGATGACGAAGCATCCACCACTGC +CTC + +>gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds +ATGAACGGGACCGAGGGCCCAAACTTCTACGTGCCTTTCTCCAACAAGACGGGCGTCGTACGCAGCCCCT +TCGAGGCGCCGCAGTACTACCTGGCTGAGCCATGGCAGTTCAGCATGCTGGCCGCCTACATGTTCCTGCT +GATCATGCTTGGCTTCCCCATCAACTTCCTCACGCTGTACGTCACAGTCCAGCACAAGAAGCTGAGGACC +CCCCTCAACTACATCCTGCTCAACCTGGCCGTGGCAGATCTCTTCATGGTGTTCGGGGGCTTCACCACCA +CCCTGTATACCTCTCTGCACGGGTACTTCGTGTTCGGTCCGACGGGCTGCAACCTCGAGGGCTTCTTTGC +CACCTTAGGCGGTGAAATTGCACTGTGGTCCTTGGTGGTGCTAGCCATCGAGCGGTACGTAGTGGTGTGC +AAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCGTCGCATTCACCTGGGTCATGG +CTCTGGCCTGTGCGGCCCCCCCCCTCGTCGGCTGGTCTAGATACATCCCGGAGGGGATGCAGTGCTCGTG +CGGGATCGATTACTACACGCCCCACGAGGAGACCAACAATGAGTCGTTCGTCATCTACATGTTCGTTGTA +CACTTCATCATCCCCCTGATTGTCATATTCTTCTGCTACGGGCAGCTGGTCTTCACCGTCAAGGAGGCTG +CAGCCCAGCAGCAGGAGTCGGCCACCACTCAGAAGGCCGAGAAGGAGGTCACGCGTATGGTCATCATCAT +GGTCATCGCTTTCCTCATATGCTGGCTGCCCTACGCAGGTGTGGCGTTCTACATCTTCACCCATCAGGGA +TCCGACTTTGGCCCCATCTTCATGACCATCCCGGCTTTCTTTGCCAAGACGTCTGCCGTCTATAACCCCG +TCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGGTCACCACTCTCTGCTGTGGCAAGAACCC +CCTAGGTGACGACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCCTGCCTAA + +>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds +CCGCTACTGACGAACCGCAACCATGAACGGCACTGAGGGACCTAACTTCTACATCCCCATGTCAAACGCC +ACTGGTGTAGTGAGGAGTCCATTTGAATACCCGCAGTACTACCTTGCAGAACCATGGGCTTTCTCAGCTC +TGTCTGCCTACATGTTCTTCCTGATTATCGCCGGATTCCCCATCAACTTCCTCACCCTGTATGTCACCAT +CGAACATAAGAAACTGAGGACCCCACTGAACTACATTCTGCTGAACCTGGCCGTGGCCGACCTCTTCATG +GTGTTTGGCGGATTCACCACCACGATGTACACCTCCATGCACGGCTACTTTGTCTTCGGCCCCACCGGCT +GCAACATCGAAGGGTTCTTCGCCACCCTCGGCGGCGAGATTGCCCTCTGGTGCCTCGTTGTCCTGGCCAT +TGAAAGGTGGATGGTCGTCTGCAAGCCAGTGACCAATTTCCGCTTCGGTGAGAGCCATGCCATCATGGGT +GTCATGGTGACCTGGACCATGGCATTGGCCTGTGCCCTCCCCCCTCTCTTCGGCTGGTCTCGGTACATTC +CGGAAGGTCTGCAGTGCTCGTGCGGGATCGACTACTATACCCGGGCGCCTGGGATCAACAATGAGTCCTT +TGTGATCTACATGTTTACCTGCCACTTCTCCATCCCACTCGCCGTCATCTCTTTCTGCTACGGCCGACTG +GTGTGCACCGTCAAAGAGGCCGCTGCCCAGCAACAGGAGTCCGAGACCACCCAGAGGGCTGAGCGGGAGG +TCACCCGCATGGTCGTCATCATGGTCATCTCCTTCCTGGTCTGCTGGGTGCCCTATGCCAGTGTGGCCTG +GTACATCTTTACCCACCAGGGAAGCACTTTTGGGCCCATCTTCATGACCATTCCATCCTTCTTTGCCAAG +AGTTCAGCCCTCTACAACCCCATGATCTACATCTGCATGAACAAGCAGTTCCGCCATTGCATGATCACCA +CCCTCTGCTGTGGGAAGAACCCCTTCGAGGAGGAGGATGGAGCGTCCGCCACTAGCTCTAAAACTGAGGC +TTCATCCGTGTCCTCCAGCTCTGTCTCCCCGGCATAAACCTTGTTTGACCGAACACCACGCATCAACACA +AAGACCAAGAATGCTGACTAAATGCTAACATTTCAGGGAAATCCAAAGACTTTTTACTATTTTTTTACAC +AACCATATAGGTTGCAAACAGAGGTTTAGCCCTGTTTACAGGTTGTCATCAATGTGATGTCAGTATGTAC +AATATAGTCAACTTGATAGCAAGTTGTTGGCTTATTTCAGATTGTATGGGCAATGTAATCAACCATATGT +GAAATAAATTGCAA diff -r 000000000000 -r 432ea9614cc9 test-data/rhodopsin_proteins.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rhodopsin_proteins.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,43 @@ +>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] +MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT +PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC +KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVV +HFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG +SNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA + +>gi|3024260|sp|P56514.1|OPSD_BUFBU RecName: Full=Rhodopsin +MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRT +PLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVC +KPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVV +HFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQG +SEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTEASSVSSSQ +VSPA + +>gi|283855846|gb|ADB45242.1| rhodopsin [Cynopterus brachyotis] +VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE +NHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF +FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTL +PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + +>gi|283855823|gb|ADB45229.1| rhodopsin [Myotis pilosus] +VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLA +VANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGE +NHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIF +FCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTI +PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS + +>gi|223523|prf||0811197A rhodopsin [Bos taurus] +MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRT +PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC +KPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYTPHEETNNESFVIYMFVVH +FIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGS +DFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + +>gi|12583665|dbj|BAB21486.1| fresh water form rod opsin [Conger myriaster] +MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRT +PLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVC +KPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTC +HFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQG +STFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTEASSVSSSS +VSPA diff -r 000000000000 -r 432ea9614cc9 test-data/segmasker_four_human.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segmasker_four_human.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,61 @@ +>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 +MHPAVFlslpdlrcsllllVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF +SQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMK +REYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFER +VANILHDDCAFLSAFGDVSKPERYSGDNIIYKPPGHSAPDMVYLGAMTNFDVTYNWIQDK +CVPLVREITFENGEELTEEGLPFLILFHMKEDTESLEIFQNEVARQLISEKGTINFLHAD +CDKFRHPLLHIQKTPADCPVIAIDSFRHMYVFGDFKDVLIPGKLKQFVFDLHSGKLHREF +HHGPDPTDTAPGEQAQDVASSPPESSFQKLAPSEYRYTLLRDRDEL +>sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 +MKKFSRMPKSEggsgggaagggaggagagagcgsggssvgvrvfavgRHQVTLEESLAEG +GFSTVFLVRTHGGIRCALKRMYVNNMPDLNVCKREITIMKELSGHKNIVGYLDCAVNSIS +DNVWEVLILMEYCRAGQVVNQMNKKLQTGFTEPEVLQIFCDTCEAVARLHQCKTPIIHRD +LKVENILLNDGGNYVLCDFGSATNKFLNPQKDGVNVVEEEIKKYTTLSYRAPEMINLYGG +KPITTKADIWALGCLLYKLCFFTLPFGESQVAICDGNFTIPDNSRYSRNIHCLIRFMLEP +DPEHRPDIFQVSYFAFKFAKKDCPVsninnssiPSALPEPMTASEAAARKSQIKARITDT +IGPTETSIAPRQRPKANSATTATPSVLTIQSSATPVKVLAPGEFGNHRPKGALRPGNGPE +Illgqgppqqppqqhrvlqqlqqgdwrlqqlhlqhrhphqqqqqqqqqqqqqqqqqqqqq +qqqqqqhhhhhhhhllqDAYMqqyqhatqqqqmlqqqFLMHSVYQPQPSASQYPTMmpqy +qqaffqqqmlaqhqpsqqqASPEYLTSPQEFSPALVSYTSSLPAQVGTIMDSSYSANRSV +ADKEAIANFTNQKNISNPPDMSGWNPFGEDNFSKLTeeelldrefdllrSNRLEERASSD +KNVDSLSAPHNHPPEDPFGSVPFISHSGSPEKKAEHSSINQENGTANPIKNGKTSPASKD +QRTGKKTSVQGQVQKGNdesesdfesdppspksseeeeqddeeVLQGEQGDFNDDDTEPE +NLGHRPLLMdsedeeeeekhssdsdyeQAKAKYSDMSSVYRDRSGSGPTQDLNTILLTSA +QLSSDVAVETPKQEFDVFGAVPFFAVRAQQPQQEKNEKNLPQHRFPAAGLEQEEFDVFTK +APFSKKVNVQECHAVGPEAHTIPGYPKSVDVFGSTPFQPFLTSTSKSESNEDLFGLVPFD +EITGSQQQKVkqrslqklssrqrrTKQDMSKSNGKRHHGtptstkktlkptYRTPERARR +HKKVGRRDSQSSNEFLTISDSKENISVALTDGKDRGNVLQPEESLLDPFGAKPFHSPDLS +WHPPHQGLSDIRADHNTVLPGRPRQNSLHGSFHSADVLKMDDFGAVPFTELVVQSITPHQ +SQQSQPVELDPFGAAPFPSKQ +>sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 +MATggrrgaaaapllvavaalllgaagHLYPGEVCPGMDIRNNLTRLHELENCSVIEGHL +QILLMFKTRPEDFRDLSFPKLIMITDYLLLFRVYGLESLKDLFPNLTVIRGSRLFFNYAL +VIFEMVHLKELGLYNLMNITRGSVRIEKNNELCYLATIDWSRILDSVEDNYIVLNKDDNE +ECGDICPGTAKGKTNCPATVINGQFVERCWTHSHCQKVCPTICKSHGCTAEGLCCHSECL +GNCSQPDDPTKCVACRNFYLDGRCVETCPPPYYHFQDWRCVNFSFCQDLHHKCKNSRRQG +CHQYVIHNNKCIPECPSGYTMNSSNLLCTPCLGPCPKVCHLLEGEKTIDSVTSAQELRGC +TVINGSLIINIRggnnlaaeleanlglieeiSGYLKIRRSYALVSLSFFRKLRLIRGETL +EIGNYSFYALDNQNLRQLWDWSKHNLTITQGKLFFHYNPKLCLSEIHKMEEVSGTKGRQE +RNDIALKTNGDQASCENELLKFSYIRTSFDKILLRWEPYWPPDFRDLLGFMLFYKEAPYQ +NVTEFDGQDACGSNSWTVVDIDPPLRSNDPKSQNHPGWLMRGLKPWTQYAIFVKTLVTFS +DERRTYGAKSDIIYVQTDATNPSVPLDPISVSNSSSQIILKWKPPSDPNGNITHYLVFWE +RQAEDSELFELDYCLKGLKLPSRTWSPPFESEDSQKHNQSEYEDSAGECCSCPKTDSQIL +KELEESSFRKTFEDYLHNVVFVPRKTSSGTGAEDPRPSRKRRSLGDvgnvtvavptvaaf +pntsstsvptspEEHRPFEKVVNKESLVISGLRHFTGYRIELQACNQDTPEERCSVAAYV +SARTMPEAKADDIVGPVTHEIFENNVVHLMWQEPKEPNGLIVLYEVSYRRYGDEELHLCV +SRKHFALERGCRLRGLSPGNYSVRIRATSLAGNGSWTEPTYFYVTDYLDVPSNIAKIIIG +PLIFVFLFSVVIGSIYLFLRKRQPDGPLGPLYASSNPEYLSASDVFPCSVYVPDEWEVSR +EKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKG +FTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAENNPGRPPPTLQEMIQMA +AEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDIYETDYYRKGGKGLLPV +RWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQVLKFVMDGGYLDQPDN +CPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFFHSEENKAPeseeleme +fedmeNVPLDRSSHCQREEAGGRDGGSSLGFKRSYEEHIPYTHMNGGKKNGRILTLPRSN +PS +>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 +MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY +VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG +GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP +EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVkeaaaqqqes +attqkaeKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI +YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA diff -r 000000000000 -r 432ea9614cc9 test-data/segmasker_four_human.maskinfo-asn1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segmasker_four_human.maskinfo-asn1 Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,114 @@ +Blast-db-mask-info ::= { + algo-id 1, + algo-program seg, + algo-options "window=12; locut=2.2; hicut=2.5", + masks { + masks { + int { + from 6, + to 18, + id local id 1 + }, + packed-int { + { + from 11, + to 46, + id local id 2 + }, + { + from 325, + to 332, + id local id 2 + }, + { + from 421, + to 443, + id local id 2 + }, + { + from 437, + to 450, + id local id 2 + }, + { + from 447, + to 496, + id local id 2 + }, + { + from 501, + to 516, + id local id 2 + }, + { + from 536, + to 554, + id local id 2 + }, + { + from 545, + to 558, + id local id 2 + }, + { + from 636, + to 648, + id local id 2 + }, + { + from 737, + to 762, + id local id 2 + }, + { + from 789, + to 806, + id local id 2 + }, + { + from 970, + to 983, + id local id 2 + }, + { + from 999, + to 1010, + id local id 2 + } + }, + packed-int { + { + from 3, + to 26, + id local id 3 + }, + { + from 372, + to 390, + id local id 3 + }, + { + from 766, + to 782, + id local id 3 + }, + { + from 780, + to 791, + id local id 3 + }, + { + from 1312, + to 1324, + id local id 3 + } + }, + int { + from 230, + to 246, + id local id 4 + } + }, + more FALSE + } +} diff -r 000000000000 -r 432ea9614cc9 test-data/segmasker_four_human.maskinfo-asn1-binary Binary file test-data/segmasker_four_human.maskinfo-asn1-binary has changed diff -r 000000000000 -r 432ea9614cc9 test-data/tblastn_four_human_vs_rhodopsin.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,787 @@ + +BLAST Search Results + +

+
+TBLASTN 2.2.30+
+
+
+Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
+OS=Homo sapiens GN=ERP44 PE=1 SV=1
+
+Length=406
+
+Subject= gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
+
+Length=1047
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 127710
+
+
+Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
+OS=Homo sapiens GN=ERP44 PE=1 SV=1
+
+Length=406
+
+Subject= gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
+cds
+
+Length=1574
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 127710
+
+
+Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
+OS=Homo sapiens GN=ERP44 PE=1 SV=1
+
+Length=406
+
+Subject= gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
+rhodopsin (RHO) gene, exons 1 through 5 and partial cds
+
+Length=4301
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 127710
+
+
+Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
+OS=Homo sapiens GN=ERP44 PE=1 SV=1
+
+Length=406
+
+Subject= gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
+(RHO) mRNA, partial cds
+
+Length=983
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 127710
+
+
+Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
+OS=Homo sapiens GN=ERP44 PE=1 SV=1
+
+Length=406
+
+Subject= gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
+rhodopsin, complete cds
+
+Length=1047
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 127710
+
+
+Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
+OS=Homo sapiens GN=ERP44 PE=1 SV=1
+
+Length=406
+
+Subject= gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
+water form rod opsin, complete cds
+
+Length=1344
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 127710
+
+
+Query= sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
+GN=BMP2K PE=1 SV=2
+
+Length=1161
+
+Subject= gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
+
+Length=1047
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 370988
+
+
+Query= sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
+GN=BMP2K PE=1 SV=2
+
+Length=1161
+
+Subject= gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
+cds
+
+Length=1574
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 370988
+
+
+Query= sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
+GN=BMP2K PE=1 SV=2
+
+Length=1161
+
+Subject= gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
+rhodopsin (RHO) gene, exons 1 through 5 and partial cds
+
+Length=4301
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 370988
+
+
+Query= sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
+GN=BMP2K PE=1 SV=2
+
+Length=1161
+
+Subject= gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
+(RHO) mRNA, partial cds
+
+Length=983
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 370988
+
+
+Query= sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
+GN=BMP2K PE=1 SV=2
+
+Length=1161
+
+Subject= gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
+rhodopsin, complete cds
+
+Length=1047
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 370988
+
+
+Query= sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens
+GN=BMP2K PE=1 SV=2
+
+Length=1161
+
+Subject= gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
+water form rod opsin, complete cds
+
+Length=1344
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 370988
+
+
+Query= sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
+SV=4
+
+Length=1382
+
+Subject= gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
+
+Length=1047
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 441350
+
+
+Query= sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
+SV=4
+
+Length=1382
+
+Subject= gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
+cds
+
+Length=1574
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 441350
+
+
+Query= sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
+SV=4
+
+Length=1382
+
+Subject= gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
+rhodopsin (RHO) gene, exons 1 through 5 and partial cds
+
+Length=4301
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 441350
+
+
+Query= sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
+SV=4
+
+Length=1382
+
+Subject= gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
+(RHO) mRNA, partial cds
+
+Length=983
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 441350
+
+
+Query= sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
+SV=4
+
+Length=1382
+
+Subject= gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
+rhodopsin, complete cds
+
+Length=1047
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 441350
+
+
+Query= sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1
+SV=4
+
+Length=1382
+
+Subject= gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
+water form rod opsin, complete cds
+
+Length=1344
+
+
+***** No hits found *****
+
+
+
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 441350
+
+
+Query= sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+
+Length=348
+
+Subject= gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA
+
+Length=1047
+
+
+ Score =   732 bits (1689),  Expect = 0.0, Method: Compositional matrix adjust.
+ Identities = 336/348 (97%), Positives = 343/348 (99%), Gaps = 0/348 (0%)
+ Frame = +1
+
+Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
+             MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY
+Sbjct  1     MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  180
+
+Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
+             VTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLG
+Sbjct  181   VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG  360
+
+Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
+             GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIP
+Sbjct  361   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP  540
+
+Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
+             EG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQES
+Sbjct  541   EGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQES  720
+
+Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
+             ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++I
+Sbjct  721   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSI  900
+
+Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA  348
+             YNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA
+Sbjct  901   YNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA  1044
+
+
+
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 109230
+
+
+Query= sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+
+Length=348
+
+Subject= gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete
+cds
+
+Length=1574
+
+
+ Score =   646 bits (1489),  Expect = 0.0, Method: Compositional matrix adjust.
+ Identities = 290/342 (85%), Positives = 320/342 (94%), Gaps = 1/342 (0%)
+ Frame = +3
+
+Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
+             MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLY
+Sbjct  42    MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLY  221
+
+Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
+             VT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLG
+Sbjct  222   VTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLG  401
+
+Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
+             GEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIP
+Sbjct  402   GEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIP  581
+
+Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
+             EG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQES
+Sbjct  582   EGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQES  761
+
+Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
+             ATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++I
+Sbjct  762   ATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSI  941
+
+Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE  341
+             YNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA  SKTE
+Sbjct  942   YNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE  1067
+
+
+
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 109230
+
+
+Query= sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+
+Length=348
+
+Subject= gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434
+rhodopsin (RHO) gene, exons 1 through 5 and partial cds
+
+Length=4301
+
+
+ Score =   151 bits (342),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
+ Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
+ Frame = +3
+
+Query  239   ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA  298
+             ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS+
+Sbjct  3147  ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSS  3326
+
+Query  299   AIYNPVIYIMMNKQ  312
+             +IYNPVIYIMMNKQ
+Sbjct  3327  SIYNPVIYIMMNKQ  3368
+
+
+ Score =   126 bits (284),  Expect(2) = 1e-72, Method: Compositional matrix adjust.
+ Identities = 54/59 (92%), Positives = 57/59 (97%), Gaps = 0/59 (0%)
+ Frame = +2
+
+Query  177   RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA  235
+             RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE  +
+Sbjct  2855  RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS  3031
+
+
+ Score =   229 bits (523),  Expect = 9e-67, Method: Compositional matrix adjust.
+ Identities = 107/111 (96%), Positives = 109/111 (98%), Gaps = 0/111 (0%)
+ Frame = +1
+
+Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
+            VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
+Sbjct  1    VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  180
+
+Query  71   PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG  121
+            PLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG
+Sbjct  181  PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG  333
+
+
+ Score =   122 bits (276),  Expect = 1e-32, Method: Compositional matrix adjust.
+ Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
+ Frame = +3
+
+Query  119   LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR  177
+             L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR
+Sbjct  1404  LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR  1580
+
+
+ Score = 57.7 bits (125),  Expect = 2e-12, Method: Compositional matrix adjust.
+ Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%)
+ Frame = +1
+
+Query  312   QFRNCMLTTICCGKNPLGDDEASATV  337
+             QFRNCMLTT+CCGKNPLGDDEAS T 
+Sbjct  4222  QFRNCMLTTLCCGKNPLGDDEASTTA  4299
+
+
+
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 109230
+
+
+Query= sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+
+Length=348
+
+Subject= gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin
+(RHO) mRNA, partial cds
+
+Length=983
+
+
+ Score =   658 bits (1517),  Expect = 0.0, Method: Compositional matrix adjust.
+ Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
+ Frame = +1
+
+Query  11   VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  70
+            VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
+Sbjct  1    VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT  180
+
+Query  71   PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVV  130
+            PLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVV
+Sbjct  181  PLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVV  360
+
+Query  131  LAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGID  190
+            LAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGID
+Sbjct  361  LAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGID  540
+
+Query  191  YYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV  250
+            YYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEV
+Sbjct  541  YYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEV  720
+
+Query  251  TRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMN  310
+            TRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMN
+Sbjct  721  TRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMN  900
+
+Query  311  KQFRNCMLTTICCGKNPLGDDEASAT  336
+            KQFRNCMLTT+CCGKNPLGDDEAS T
+Sbjct  901  KQFRNCMLTTLCCGKNPLGDDEASTT  978
+
+
+
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 109230
+
+
+Query= sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+
+Length=348
+
+Subject= gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for
+rhodopsin, complete cds
+
+Length=1047
+
+
+ Score =   711 bits (1640),  Expect = 0.0, Method: Compositional matrix adjust.
+ Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
+ Frame = +1
+
+Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
+             MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLY
+Sbjct  1     MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY  180
+
+Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
+             VTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLG
+Sbjct  181   VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG  360
+
+Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
+             GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIP
+Sbjct  361   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP  540
+
+Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
+             EG+QCSCGIDYYT   E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQES
+Sbjct  541   EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES  720
+
+Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
+             ATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+
+Sbjct  721   ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV  900
+
+Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA  348
+             YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA
+Sbjct  901   YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA  1044
+
+
+
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 109230
+
+
+Query= sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1
+
+Length=348
+
+Subject= gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh
+water form rod opsin, complete cds
+
+Length=1344
+
+
+ Score =   626 bits (1444),  Expect = 0.0, Method: Compositional matrix adjust.
+ Identities = 281/342 (82%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
+ Frame = +2
+
+Query  1     MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY  60
+             MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLY
+Sbjct  23    MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLY  202
+
+Query  61    VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG  120
+             VT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLG
+Sbjct  203   VTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLG  382
+
+Query  121   GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIP  180
+             GEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV  TW MALACA PPL GWSRYIP
+Sbjct  383   GEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIP  562
+
+Query  181   EGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQES  240
+             EGLQCSCGIDYYT  P +NNESFVIYMF  HF+IP+ +I FCYG+LV TVKEAAAQQQES
+Sbjct  563   EGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQES  742
+
+Query  241   ATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAI  300
+              TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+
+Sbjct  743   ETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSAL  922
+
+Query  301   YNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE  341
+             YNP+IYI MNKQFR CM+TT+CCGKNP   +D ASAT SKTE
+Sbjct  923   YNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE  1048
+
+
+
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
+
+Gapped
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
+
+Effective search space used: 109230
+
+
+
+
+Matrix: BLOSUM80
+Gap Penalties: Existence: 10, Extension: 1
+Neighboring words threshold: 14
+Window for multiple hits: 25
+

+ + diff -r 000000000000 -r 432ea9614cc9 test-data/tblastn_four_human_vs_rhodopsin.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,10 @@ +sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0 732 +sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 +sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 +sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626 diff -r 000000000000 -r 432ea9614cc9 test-data/tblastn_four_human_vs_rhodopsin.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,741 @@ + + + + tblastn + TBLASTN 2.2.30+ + Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. + + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + BLOSUM80 + 1e-10 + 10 + 1 + F + + + + + 1 + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 19 + 127710 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 2 + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 19 + 127710 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 3 + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 19 + 127710 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 4 + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 19 + 127710 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 5 + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 19 + 127710 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 6 + Query_1 + sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + 406 + + + + + 0 + 0 + 19 + 127710 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 7 + Query_2 + sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 23 + 370988 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 8 + Query_2 + sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 23 + 370988 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 9 + Query_2 + sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 23 + 370988 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 10 + Query_2 + sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 23 + 370988 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 11 + Query_2 + sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 23 + 370988 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 12 + Query_2 + sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens GN=BMP2K PE=1 SV=2 + 1161 + + + + + 0 + 0 + 23 + 370988 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 13 + Query_3 + sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 24 + 441350 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 14 + Query_3 + sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 24 + 441350 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 15 + Query_3 + sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 24 + 441350 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 16 + Query_3 + sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 24 + 441350 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 17 + Query_3 + sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 24 + 441350 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 18 + Query_3 + sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 SV=4 + 1382 + + + + + 0 + 0 + 24 + 441350 + 0.071 + 0.299 + 0.27 + + + No hits found + + + 19 + Query_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + Subject_1 + gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + Subject_1 + 1047 + + + 1 + 732.393 + 1689 + 0 + 1 + 348 + 1 + 1044 + 0 + 1 + 336 + 343 + 0 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T SKTETSQVAPA + + + + + + + 0 + 0 + 18 + 109230 + 0.071 + 0.299 + 0.27 + + + + + 20 + Query_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + Subject_2 + gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds + Subject_2 + 1574 + + + 1 + 646.12 + 1489 + 0 + 1 + 341 + 42 + 1067 + 0 + 3 + 290 + 320 + 1 + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE + MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE + MNGTEGPNFY+P SN TGVVRSPFEYPQYYLAEPWQ+S+L AYMFLLI+LGFPINF+TLYVT+QHKKLRTPLNYILLNLA A+ FMVL GFT T+Y+S+ GYF+ G TGC +EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRF ENHA+MGVAFTW+MAL+CA PPL GWSRYIPEG+QCSCG+DYYTLKPEVNNESFVIYMFVVHFTIP+IIIFFCYG+LV TVKEAAAQQQESATTQKAEKEVTRMVIIMV+ FLICWVPYASVAF+IF+ QGS FGPIFMT+PAFFAKS++IYNPVIYIM+NKQFRNCM+TT+CCGKNP G+D+A SA SKTE + + + + + + + 0 + 0 + 18 + 109230 + 0.071 + 0.299 + 0.27 + + + + + 21 + Query_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + Subject_3 + gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 rhodopsin (RHO) gene, exons 1 through 5 and partial cds + Subject_3 + 4301 + + + 1 + 151.343 + 342 + 1.39567e-72 + 239 + 312 + 3147 + 3368 + 0 + 3 + 69 + 73 + 0 + 74 + ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ + ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ + ESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGSNFGPIFMT+PAFFAKS++IYNPVIYIMMNKQ + + + 2 + 126.324 + 284 + 1.39567e-72 + 177 + 235 + 2855 + 3031 + 0 + 2 + 54 + 57 + 0 + 59 + RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA + RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS + RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE + + + + 3 + 229.42 + 523 + 9.34154e-67 + 11 + 121 + 1 + 333 + 0 + 1 + 107 + 109 + 0 + 111 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG + VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG + VPFSN TGVVRSPFE+PQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGG + + + 4 + 122.873 + 276 + 1.03783e-32 + 119 + 177 + 1404 + 1580 + 0 + 3 + 55 + 56 + 0 + 59 + LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR + LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR + L GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+A TWVMALACAAPPL GWSR + + + 5 + 57.7368 + 125 + 1.50808e-12 + 312 + 337 + 4222 + 4299 + 0 + 1 + 23 + 24 + 0 + 26 + QFRNCMLTTICCGKNPLGDDEASATV + QFRNCMLTTLCCGKNPLGDDEASTTA + QFRNCMLTT+CCGKNPLGDDEAS T + + + + + + + 0 + 0 + 18 + 109230 + 0.071 + 0.299 + 0.27 + + + + + 22 + Query_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + Subject_4 + gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin (RHO) mRNA, partial cds + Subject_4 + 983 + + + 1 + 658.198 + 1517 + 0 + 11 + 336 + 1 + 978 + 0 + 1 + 310 + 322 + 0 + 326 + VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT + VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT + VPFSN TGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVA+LFMV GGFT+TLYTS+HGYFVFG TGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMG+AFTWVMALACAAPPLAGWSRYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMV+AFLICW+PYASVAFYIFTHQGSNFGP+FMTIPAFFAKS++IYNPVIYIMMNKQFRNCMLTT+CCGKNPLGDDEAS T + + + + + + + 0 + 0 + 18 + 109230 + 0.071 + 0.299 + 0.27 + + + + + 23 + Query_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + Subject_5 + gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for rhodopsin, complete cds + Subject_5 + 1047 + + + 1 + 711.256 + 1640 + 0 + 1 + 348 + 1 + 1044 + 0 + 1 + 325 + 337 + 0 + 348 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA + MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA + MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA + + + + + + + 0 + 0 + 18 + 109230 + 0.071 + 0.299 + 0.27 + + + + + 24 + Query_4 + sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + 348 + + + 1 + Subject_6 + gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds + Subject_6 + 1344 + + + 1 + 626.708 + 1444 + 0 + 1 + 341 + 23 + 1048 + 0 + 2 + 281 + 311 + 1 + 342 + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE + MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE + MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP +D ASAT SKTE + + + + + + + 0 + 0 + 18 + 109230 + 0.071 + 0.299 + 0.27 + + + + + + diff -r 000000000000 -r 432ea9614cc9 test-data/tblastn_four_human_vs_rhodopsin_ext.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,10 @@ +sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0 732 gi|57163782|ref|NM_001009242.1| 1689 336 343 0 98.56 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA 348 1047 N/A +sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 gi|283855845|gb|GQ290303.1| 284 54 57 0 96.61 0 2 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 gi|283855845|gb|GQ290303.1| 276 55 56 0 94.92 0 3 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301 N/A +sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983 N/A +sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047 N/A +sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344 N/A diff -r 000000000000 -r 432ea9614cc9 test-data/tblastx_rhodopsin_vs_three_human.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastx_rhodopsin_vs_three_human.tabular Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,117 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 97.39 230 6 0 1 690 88 777 0.0 559 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 94.12 102 6 0 742 1047 829 1134 0.0 236 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 91.22 148 13 0 1046 603 1133 690 0.0 308 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 94.32 88 5 0 566 303 653 390 0.0 207 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 96.34 82 3 0 248 3 335 90 0.0 182 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 83.33 204 34 0 18 629 105 716 4e-158 404 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 75.28 89 22 0 780 1046 867 1133 4e-158 161 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 81.28 203 38 0 609 1 696 88 5e-153 360 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 80.60 67 13 0 916 716 1003 803 5e-153 135 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 70.27 37 11 0 1047 937 1134 1024 5e-153 64.2 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 100.00 7 0 0 646 626 733 713 5e-153 24.0 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 89.23 65 7 0 460 266 547 353 4e-105 167 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 89.58 48 5 0 184 41 271 128 4e-105 104 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 77.78 45 10 0 882 748 969 835 4e-105 93.9 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 67.86 28 9 0 1045 962 1132 1049 4e-105 51.9 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 59.09 22 9 0 586 521 673 608 4e-105 33.1 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 81.40 86 16 0 296 553 383 640 2e-87 185 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 84.38 32 5 0 11 106 98 193 2e-87 74.8 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 71.43 35 10 0 941 1045 1028 1132 2e-87 61.6 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 94.44 18 1 0 794 847 881 934 2e-87 50.1 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 83.61 238 39 0 18 731 64 777 0.0 507 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 82.35 85 15 0 783 1037 829 1083 0.0 188 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 70.96 303 88 0 925 17 971 63 2e-130 435 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 72.22 18 5 0 1027 974 1073 1020 2e-130 35.0 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 55.32 188 84 0 605 42 651 88 7e-89 245 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 61.11 72 28 0 1037 822 1083 868 7e-89 91.3 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 49.02 204 104 0 29 640 75 686 4e-78 197 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 66.04 53 18 0 860 1018 906 1064 4e-78 85.8 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 44.44 27 15 0 689 769 735 815 4e-78 32.2 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 47.47 198 104 0 633 40 679 86 4e-65 177 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 68.09 47 15 0 1017 877 1063 923 4e-65 80.3 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 57.89 114 48 0 265 606 311 652 3e-46 137 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 46.30 54 29 0 19 180 65 226 3e-46 52.4 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 96.40 111 4 0 1 333 118 450 0.0 264 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.31 65 5 0 3174 3368 829 1023 0.0 151 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 96.43 56 2 0 2855 3022 616 783 0.0 141 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 93.22 59 4 0 1404 1580 442 618 0.0 138 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.00 25 2 0 4222 4296 1021 1095 0.0 64.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 88.89 9 1 0 3128 3154 783 809 0.0 22.6 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 78.38 111 24 0 333 1 450 118 7e-171 212 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 88.75 80 9 0 3367 3128 1022 783 7e-171 161 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 93.33 60 4 0 1582 1403 620 441 7e-171 136 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.07 56 5 0 3021 2854 782 615 7e-171 119 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 84.62 26 4 0 4301 4224 1100 1023 7e-171 52.8 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 95.83 72 3 0 218 3 335 120 8e-142 152 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 77.78 63 14 0 3368 3180 1023 835 8e-142 125 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 85.11 47 7 0 1544 1404 582 442 8e-142 108 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.36 56 11 0 3022 2855 783 616 8e-142 101 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 75.86 29 7 0 325 239 442 356 8e-142 58.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 86.36 22 3 0 4287 4222 1086 1021 8e-142 48.7 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 90.91 11 1 0 3159 3127 814 782 8e-142 31.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 81.03 58 11 0 2854 3027 615 788 2e-122 128 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 83.33 60 10 0 1403 1582 441 620 2e-122 125 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.60 67 13 0 3 203 120 320 2e-122 119 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.30 23 2 0 4220 4288 1019 1087 2e-122 53.8 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 78.26 23 5 0 266 334 383 451 2e-122 48.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.00 20 4 0 3308 3367 963 1022 2e-122 46.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 83.33 18 3 0 3226 3279 881 934 2e-122 40.5 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.39 51 10 0 154 2 271 119 1e-92 97.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 73.68 57 15 0 3366 3196 1021 851 1e-92 95.9 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 81.82 44 8 0 1521 1390 559 428 1e-92 95.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 95.00 20 1 0 332 273 449 390 1e-92 52.4 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 86.36 22 3 0 4288 4223 1087 1022 1e-92 48.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 61.54 26 10 0 2912 2835 673 596 1e-92 37.7 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 69.57 23 7 0 3023 2955 784 716 1e-92 33.1 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 76.67 30 7 0 2 91 119 208 6e-43 68.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.11 45 4 0 1411 1545 449 583 6e-43 68.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 77.27 22 5 0 267 332 384 449 6e-43 45.1 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 86.36 22 3 0 4224 4289 1023 1088 6e-43 44.1 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 83.33 12 2 0 2856 2891 617 652 6e-43 25.4 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 95.91 220 9 0 1 660 118 777 0.0 526 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 92.13 89 7 0 712 978 829 1095 0.0 212 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.01 178 16 0 536 3 653 120 1e-178 353 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 88.32 137 16 0 983 573 1100 690 1e-178 277 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 77.43 319 72 0 3 959 120 1076 4e-174 593 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 79.07 129 27 0 558 172 675 289 2e-133 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 76.83 82 19 0 963 718 1080 835 2e-133 159 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 84.09 44 7 0 133 2 250 119 2e-133 97.3 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 73.08 78 21 0 433 200 550 317 6e-102 145 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 70.15 67 20 0 799 599 916 716 6e-102 106 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 80.49 41 8 0 123 1 240 118 6e-102 84.5 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 77.78 27 6 0 553 473 670 590 6e-102 51.9 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 71.43 14 4 0 889 848 1006 965 6e-102 32.7 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 81.82 11 2 0 958 926 1075 1043 6e-102 28.6 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 84.85 33 5 0 239 337 356 454 4e-48 72.5 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 86.67 30 4 0 2 91 119 208 4e-48 71.2 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 81.40 43 8 0 404 532 521 649 4e-48 47.3 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 88.89 18 2 0 764 817 881 934 4e-48 44.6 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 87.50 8 1 0 935 958 1052 1075 4e-48 21.7 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 93.91 230 14 0 1 690 88 777 0.0 538 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 91.18 102 9 0 742 1047 829 1134 0.0 233 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 88.83 188 21 0 566 3 653 90 0.0 394 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 84.06 138 22 0 1046 633 1133 720 0.0 260 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 67.11 228 75 0 684 1 771 88 7e-132 333 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 67.27 110 36 0 1045 716 1132 803 7e-132 141 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 70.20 151 45 0 3 455 90 542 1e-128 236 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 64.04 89 32 0 780 1046 867 1133 1e-128 136 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 66.22 74 25 0 510 731 597 818 1e-128 111 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 66.04 106 36 0 242 559 329 646 2e-58 161 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 85.71 21 3 0 92 154 179 241 2e-58 53.8 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 73.68 19 5 0 791 847 878 934 2e-58 39.1 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 61.29 62 24 0 424 239 511 326 4e-55 81.3 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 74.36 39 10 0 133 17 220 104 4e-55 69.8 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 65.71 35 12 0 882 778 969 865 4e-55 56.3 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 58.14 43 18 0 649 521 736 608 4e-55 50.6 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 66.67 12 4 0 972 937 1059 1024 4e-55 23.9 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 82.13 235 42 0 11 715 76 780 0.0 498 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 78.31 83 18 0 770 1018 835 1083 0.0 177 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 72.29 332 92 0 1017 22 1082 87 1e-150 516 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 48.30 147 76 0 712 272 777 337 2e-98 169 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 54.17 72 33 0 1030 815 1095 880 2e-98 103 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 47.83 69 36 0 220 14 285 79 2e-98 83.5 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 72.00 25 7 0 782 708 847 773 2e-98 45.1 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 56.00 75 33 0 532 756 597 821 5e-65 87.7 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 39.42 104 63 0 19 330 84 395 5e-65 86.8 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 56.90 58 25 0 829 1002 894 1067 5e-65 81.3 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 50.00 30 15 0 388 477 453 542 5e-65 33.6 diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.dbinfo.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.dbinfo.txt Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,7 @@ +Database: Just 3 human mRNA sequences + 3 sequences; 10,732 total bases + +Date: Dec 26, 2014 5:54 AM Longest sequence: 4,796 bases + +Volumes: + /mnt/galaxy/galaxy_blast/test-data/three_human_mRNA.fasta diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,183 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG +CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC +GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC +CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC +TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT +TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA +CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA +CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC +TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA +TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG +GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA +TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA +ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA +CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC +AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT +CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC +CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA +TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG +CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC +CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA +GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT +ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA +GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT +CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT +GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA +TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA +CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA +AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG +GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG +AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT +TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT +TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT +TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG +CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA +CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT +TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC +TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT +GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT +AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT +TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT +GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT +TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA +GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA +TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA +TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT +AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT +TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT +ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT +GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA +GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT +GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT +TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT +TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT +AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG +AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC +TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT +CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA +GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT +TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT +GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT +TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG +GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA +CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA +CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA +GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA +GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT +GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG +GAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCA +ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA +AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA +ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA +GGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGAT +AAAGTAGTGTAATGGATTGACAATCAGGAAGAACAGAATAACTCAGTTTTTTTTTCTCCT +ACAAGGAGATATGGCTGGACCAAAATAAAATGACATGAAATTGCAAAAATGAAAAT +>ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds. +GGGGGGCTGCGCGGCCGGGTCGGTGCGCACACGAGAAGGACGCGCGGCCCCCAGCGCTCT +TGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGA +CCCCGCGCTCCCGCAGCCATGGGCACCGGGGGCCGGCGGGGGGCGGCGGCCGCGCCGCTG +CTGGTGGCGGTGGCCGCGCTGCTACTGGGCGCCGCGGGCCACCTGTACCCCGGAGAGGTG +TGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCT +GTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGA +GACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTAT +GGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTG +TTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTAC +AACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTAC +TTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTG +AACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACC +AACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCAC +TGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGT +TGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCC +TGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCAC +TTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAG +AACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAG +TGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCC +TGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCC +CAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGC +AACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTAT +CTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTG +ATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAAC +CTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTC +TTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGA +ACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCC +TGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTG +AGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTAC +AAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAAC +AGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAAC +CACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAG +ACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTAT +GTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCA +TCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCAC +TACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGC +CTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT +CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG +ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT +TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC +CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG +CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG +CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC +TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC +AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT +GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG +AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG +GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT +GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC +TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT +GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT +ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT +TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC +GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC +GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG +GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG +GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC +AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC +CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA +GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG +TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA +ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC +AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC +ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA +CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT +CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA +TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG +CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT +GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC +TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC +TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG +ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT +CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT +ACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGAC +TCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAA +GGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGT +TTTTTCGTTCCCCCCACCCGCCCCCAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATT +CTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGGTGTCTGAGCTTCAGTATAAAAGACAA +AACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA +>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds. +CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGC +CACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTG +CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG +GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC +TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT +CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC +ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT +TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG +GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC +CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA +CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC +TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC +TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG +GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC +CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG +GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA +GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG +CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT +GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG +CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA +GCCATCCCACCAG diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta.log.txt Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,5 @@ +New DB title: Just 3 human mRNA sequences +Sequence type: Nucleotide +Keep Linkouts: T +Keep MBits: T +Maximum file size: 1000000000B diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nhd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta.nhd Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,3 @@ +12956943350 +13082197871 +19180330422 diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nhi Binary file test-data/three_human_mRNA.fasta.nhi has changed diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nhr Binary file test-data/three_human_mRNA.fasta.nhr has changed diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nin Binary file test-data/three_human_mRNA.fasta.nin has changed diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nog Binary file test-data/three_human_mRNA.fasta.nog has changed diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta.nsd Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,3 @@ +gnl|bl_ord_id|00 +gnl|bl_ord_id|11 +gnl|bl_ord_id|22 diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nsi Binary file test-data/three_human_mRNA.fasta.nsi has changed diff -r 000000000000 -r 432ea9614cc9 test-data/three_human_mRNA.fasta.nsq Binary file test-data/three_human_mRNA.fasta.nsq has changed diff -r 000000000000 -r 432ea9614cc9 test-data/tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tool_data_table_conf.xml.test Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,15 @@ + + + + value, name, path + +

+ + value, name, path + +

+ diff -r 000000000000 -r 432ea9614cc9 tool-data/blastdb.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blastdb.loc.sample Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,39 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of nucleotide BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +# +# +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in +#it, and that there are only two tabs on each line. +# +#So, for example, if your database is nt and the path to your base name +#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry +#would look like this: +# +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +# +#and your /depot/data2/galaxy/blastdb/nt directory would contain all of +#your "base names" (e.g.): +# +#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr +#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin +#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq +#...etc... +# +#Your blastdb.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#...etc... +# +#You can download the NCBI provided protein databases like NT from here: +#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# +#See also blastdb_p.loc which is for any protein BLAST database, and +#blastdb_d.loc which is for any protein domains databases (like CDD). + + diff -r 000000000000 -r 432ea9614cc9 tool-data/blastdb_d.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blastdb_d.loc.sample Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,35 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of protein domain databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +# +# +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in it, +#and that there are only two tabs on each line. +# +#You can download the NCBI provided databases as tar-balls from here: +#ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ +# +#So, for example, if your database is CDD and the path to your base name +#is /data/blastdb/Cdd, then the blastdb_d.loc entry would look like this: +# +#Cdd{tab}NCBI Conserved Domains Database (CDD){tab}/data/blastdb/Cdd +# +#and your /data/blastdb directory would contain all of the files associated +#with the database, /data/blastdb/Cdd.*. +# +#Your blastdb_d.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#Cdd NCBI CDD /data/blastdb/domains/Cdd +#Kog KOG (eukaryotes) /data/blastdb/domains/Kog +#Cog COG (prokaryotes) /data/blastdb/domains/Cog +#Pfam Pfam-A /data/blastdb/domains/Pfam +#Smart SMART /data/blastdb/domains/Smart +#Tigr TIGR /data/blastdb/domains/Tigr +#Prk Protein Clusters database /data/blastdb/domains/Prk +#...etc... +# +#See also blastdb.loc which is for any nucleotide BLAST database, and +#blastdb_p.loc which is for any protein BLAST databases. diff -r 000000000000 -r 432ea9614cc9 tool-data/blastdb_p.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blastdb_p.loc.sample Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of protein BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +# +# +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in +#it, and that there are only two tabs on each line. +# +#So, for example, if your database is NR and the path to your base name +#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: +# +#nr{tab}NCBI NR (non redundant){tab}/data/blastdb/nr +# +#and your /data/blastdb directory would contain all of the files associated +#with the database, /data/blastdb/nr.*. +# +#Your blastdb_p.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#...etc... +# +#You can download the NCBI provided protein databases like NR from here: +#ftp://ftp.ncbi.nlm.nih.gov/blast/db/ +# +#See also blastdb.loc which is for any nucleotide BLAST database, and +#blastdb_d.loc which is for any protein domains databases (like CDD). diff -r 000000000000 -r 432ea9614cc9 tool-data/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/tool_data_table_conf.xml.sample Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,14 @@ + + + value, name, path + +

+ + value, name, path + +

+ diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/README.rst Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,266 @@ +Galaxy wrappers for NCBI BLAST+ suite +===================================== + +These wrappers are copyright 2010-2014 by Peter Cock (The James Hutton Institute, +UK) and additional contributors including Edward Kirton, John Chilton, +Nicola Soranzo, Jim Johnson, and Bjoern Gruening. + +See the licence text below. + +Currently tested with NCBI BLAST 2.2.30+ (i.e. version 2.2.30 of BLAST+), +and does not work with the NCBI 'legacy' BLAST suite (e.g. ``blastall``). + +Note that these wrappers (and the associated datatypes) were originally +distributed as part of the main Galaxy repository, but as of August 2012 +moved to the Galaxy Tool Shed as ``ncbi_blast_plus`` (and ``blast_datatypes``). +My thanks to Dannon Baker from the Galaxy development team for his assistance +with this. + +These wrappers are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + + +Citation +======== + +Please cite the following paper (currently available as a preprint): + +NCBI BLAST+ integrated into Galaxy. +P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo +bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint) + +You should also cite the NCBI BLAST+ tools: + +BLAST+: architecture and applications. +C. Camacho et al. BMC Bioinformatics 2009, 10:421. +DOI: http://dx.doi.org/10.1186/1471-2105-10-421 + + +Automated Installation +====================== + +Galaxy should be able to automatically install the dependencies, i.e. the +BLAST+ binaries and the ``blast_datatypes`` repository which defines the +BLAST XML file format (``blastxml``), protein and nucleotide BLAST databases +(``blastdbp`` and ``blastdbn``), and so on. + +See the configuration notes below. + +Manual Installation +=================== + +For those not using Galaxy's automated installation from the Tool Shed, put +the XML and Python files in the ``tools/ncbi_blast_plus/`` folder and add the +XML files to your ``tool_conf.xml`` as normal. For example, use:: + +

+ + + + + + + + + + + + + +

+ +You will also need to install ``blast_datatypes`` from the Tool Shed. This +defines the BLAST XML file format (``blastxml``), BLAST databases, etc: + +* http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes + +As described above for an automated installation, you must also tell Galaxy +about any system level BLAST databases using the ``tool-data/blastdb*.loc`` +files. Also merge the ``tool-data/tool_data_table_conf.xml.sample`` contents +into your ``tool_data_table_conf.xml`` file. + +You must install the NCBI BLAST+ standalone tools somewhere on the system +path. Currently the unit tests are written using BLAST+ 2.2.30. + +Run the functional tests (adjusting the section identifier to match your +``tool_conf.xml.sample`` file):: + + ./run_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools + +Configuration +============= + +You must tell Galaxy about any system level BLAST databases using configuration +files ``blastdb.loc`` (nucleotide databases like NT) and ``blastdb_p.loc`` +(protein databases like NR), and ``blastdb_d.loc`` (protein domain databases +like CDD or SMART) which are located in the ``tool-data/`` folder. Sample +files are included which explain the tab-based format to use. + +You can download the NCBI provided databases as tar-balls from here: + +* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) +* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) + +If using the optional taxonomy columns, you will also need to download the +NCBI taxonomy files (``taxdb.btd`` and ``taxdb.bti`` from ``taxdb.tar.gz`` on +the BLAST database FTP site). Currently explicit version tracking of the +taxonomy is not supported, and in order to use this you must set the +``$BLASTDB`` environment variable to include the path where you unzipped the +taxonomy files. If this is not done, the taxonomy columns like species name +will appear as ``N/A`` in the tabular output. + +The BLAST+ binaries support multi-threaded operation, which is handled via the +``$GALAXY_SLOTS`` environment variable. This should be set automatically by +Galaxy via your job runner settings, which allows you to (for example) allocate +four cores to each BLAST job. + +In addition, the BLAST+ wrappers also support high level parallelism by task +splitting if ``use_tasked_jobs = True`` is enabled in your ``universe_wsgi.ini`` +configuration file. Essentially, the FASTA input query files are broken up into +batches of 1000 sequences, a separate BLAST child job is run for each chunk, +and then the BLAST output files are merged (in order). This is transparent +for the end user. + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.11 - Final revision as part of the Galaxy main repository, and the + first release via the Tool Shed +v0.0.12 - Implements genetic code option for translation searches. + - Changes ```` to 1000 sequences at a time (to cope with + very large sets of queries where BLAST+ can become memory hungry) + - Include warning that BLAST+ with subject FASTA gives pairwise + e-values +v0.0.13 - Use the new error handling options in Galaxy (the previously + bundled ``hide_stderr.py`` script is no longer needed). +v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases + in the history (using work from Edward Kirton), requires v0.0.14 + of the ``blast_datatypes`` repository from the Tool Shed. +v0.0.15 - Stronger warning in help text against searching against subject + FASTA files (better looking e-values than you might be expecting). +v0.0.16 - Added repository_dependencies.xml for automates installation of the + ``blast_datatypes`` repository from the Tool Shed. +v0.0.17 - The BLAST+ search tools now default to extended tabular output + (all too often our users where having to re-run searches just to + get one of the missing columns like query or subject length) +v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, + BLAST+ handling of some multi-file arguments is problematic). +v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new ``blastdb_d.loc`` + for the domain databases they use (e.g. CDD, PFAM or SMART). + - Correct case of exception regular expression (for error handling + fall-back in case the return code is not set properly). + - Clearer naming of output files. +v0.0.20 - Added unit tests for BLASTN and TBLASTX. + - Added percentage identity option to BLASTN. + - Fallback on ElementTree if cElementTree missing in XML to tabular. + - Link to Tool Shed added to help text and this documentation. + - Tweak dependency on ``blast_datatypes`` to also work on Test Tool Shed. + - Dependency on new ``package_blast_plus_2_2_26`` in Tool Shed. + - Adopted standard MIT License. + - Development moved to GitHub, https://github.com/peterjc/galaxy_blast + - Updated citation information (Cock et al. 2013). +v0.0.21 - Use macros to simplify the XML wrappers (by John Chilton). + - Added wrapper for dustmasker. + - Enabled masking for makeblastdb (Nicola Soranzo). + - Requires ``maskinfo-asn1`` and ``maskinfo-asn1-binary`` datatypes, + defined in ``blast_datatypes`` v0.0.17 on Galaxy ToolShed. + - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26. + - Now depends on ``package_blast_plus_2_2_27`` in ToolShed. +v0.0.22 - More use of macros to simplify the wrappers. + - Set number of threads via ``$GALAXY_SLOTS`` environment variable. + - More descriptive default output names. + - Tests require updated BLAST DB definitions (``blast_datatypes`` v0.0.18). + - Pre-check for duplicate identifiers in ``makeblastdb`` wrapper. + - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27. + - Now depends on ``package_blast_plus_2_2_28`` in ToolShed. + - Extended tabular output includes 'salltitles' as column 25. +v0.1.00 - Now depends on ``package_blast_plus_2_2_29`` in ToolShed. + - Tabular output now includes option to pick specific columns + (based on contribution from Jim Johnson), including previously + unavailable taxonomy columns. + - BLAST XML to tabular tool supports multiple input files + (based on contribution from Jim Johnson). + - More detailed descriptions for BLASTN and BLASTP task option. + - Wrappers for segmasker, dustmasker and convert2blastmask + (contribution from Bjoern Gruening). + - Supports using maskinfo with ``makeblastdb`` wrapper. + - Supports setting a taxonomy ID in ``makeblastdb`` wrapper. + - Subtle changes like new conditional settings will require some old + workflows be updated to cope. +v0.1.01 - Requires ``blastdbd`` datatype (``blast_datatypes`` v0.0.19). + - Wrapper for makeprofiledb added to create protein domain databases + (based on contribution from Bjoern Gruening). + - The RPS-BLAST and RPS-TBLASTN wrappers support using a protein + domain database from the user's history. + - Tool definitions now embed citation information (by John Chilton). + - BLAST tools support GI and SeqID filters (added by Bjoern Gruening). +v0.1.02 - Now depends on ``package_blast_plus_2_2_30`` in ToolShed. + - Tests updated for BLAST+ 2.2.30 instead of BLAST+ 2.2.29. + - New tasks ``blastp-fast``, ``blastx-fast`` and ``tblastn-fast``. + - New minimum query HSP coverage option, ``-qcov_hsp_perc``. + - Removed ``-word_size`` from RPS-BLAST and RPS-TBLASTN wrappers, this + is set during database construction and should not have been offered + as a command line option in releases prior to BLAST+ 2.2.30. + - BLAST database ``blastdb*.loc`` files now accessed via the XML + table definitions in Galaxy's ``tool_data_table_conf.xml`` file, + setup via ``tool-data/tool_data_table_conf.xml.sample`` + - Replace ``.extra_files_path`` with ``.files_path`` (internal change, + thanks to Bjoern Gruening and John Chilton). + - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. +======= ====================================================================== + + +Bug Reports +=========== + +You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask +us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev + + +Developers +========== + +This script and related tools were originally developed on the 'tools' branch +of the following Mercurial repository: +https://bitbucket.org/peterjc/galaxy-central/ + +As of July 2013, development is continuing on a dedicated GitHub repository: +https://github.com/peterjc/galaxy_blast + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the following command from the GitHub repository root folder:: + + $ tools/ncbi_blast_plus/make_ncbi_blast_plus.sh + +This simplifies ensuring a consistent set of files is bundled each time, +including all the relevant test files. + +When updating the version of BLAST+, many of the sample data files used for +the unit tests must be regenerated. This script automates that task:: + + $ tools/ncbi_blast_plus/update_test_files.sh + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/blastxml_to_tabular.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,344 @@ +#!/usr/bin/env python +"""Convert a BLAST XML file to tabular output. + +Takes three command line options, input BLAST XML filename, output tabular +BLAST filename, output format (std for standard 12 columns, or ext for the +extended 24 columns offered in the BLAST+ wrappers). + +The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart +qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which +mean: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The additional columns offered in the Galaxy BLAST+ wrappers are: + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length + 25 salltitles All subject titles, separated by '<>' +====== ============= =========================================== + +Most of these fields are given explicitly in the XML file, others some like +the percentage identity and the number of gap openings must be calculated. + +Be aware that the sequence in the extended tabular output or XML direct from +BLAST+ may or may not use XXXX masking on regions of low complexity. This +can throw the off the calculation of percentage identity and gap openings. +[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard, +with these numbers changing depending on whether or not the low complexity +filter is used.] + +This script attempts to produce identical output to what BLAST+ would have done. +However, check this with "diff -b ..." since BLAST+ sometimes includes an extra +space character (probably a bug). +""" +import sys +import re +import os +from optparse import OptionParser + +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.1.04" + sys.exit(0) + +if sys.version_info[:2] >= ( 2, 5 ): + try: + from xml.etree import cElementTree as ElementTree + except ImportError: + from xml.etree import ElementTree as ElementTree +else: + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree + +def stop_err( msg ): + sys.stderr.write("%s\n" % msg) + sys.exit(1) + +if len(sys.argv) == 4 and sys.argv[3] in ["std", "x22", "ext"]: + #False positive if user really has a BLAST XML file called 'std' or 'ext'... + stop_err("""ERROR: The script API has changed, sorry. + +Instead of the old style: + +$ python blastxml_to_tabular.py input.xml output.tabular std + +Please use: + +$ python blastxml_to_tabular.py -o output.tabular -c std input.xml + +For more information, use: + +$ python blastxml_to_tabular.py -h +""") + +usage = """usage: %prog [options] blastxml[,...] + +Convert one (or more) BLAST XML files into a single tabular file. + +The columns option can be 'std' (standard 12 columns), 'ext' +(extended 25 columns), or a list of BLAST+ column names like +'qseqid,sseqid,pident' (space or comma separated). +""" +parser = OptionParser(usage=usage) +parser.add_option('-o', '--output', dest='output', default=None, help='output filename (defaults to stdout)', metavar="FILE") +parser.add_option("-c", "--columns", dest="columns", default='std', help="[std|ext|col1,col2,...] standard 12 columns, extended 25 columns, or list of column names") +(options, args) = parser.parse_args() + +colnames = 'qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,sallseqid,score,nident,positive,gaps,ppos,qframe,sframe,qseq,sseq,qlen,slen,salltitles'.split(',') + +if len(args) < 1: + stop_err("ERROR: No BLASTXML input files given; run with --help to see options.") + +out_fmt = options.columns +if out_fmt == "std": + extended = False + cols = None +elif out_fmt == "x22": + stop_err("Format argument x22 has been replaced with ext (extended 25 columns)") +elif out_fmt == "ext": + extended = True + cols = None +else: + cols = out_fmt.replace(" ", ",").split(",") #Allow space or comma separated + #Remove any blank entries due to trailing comma, + #or annoying "None" dummy value from Galaxy if no columns + cols = [c for c in cols if c and c != "None"] + extra = set(cols).difference(colnames) + if extra: + stop_err("These are not recognised column names: %s" % ",".join(sorted(extra))) + del extra + assert set(colnames).issuperset(cols), cols + if not cols: + stop_err("No columns selected!") + extended = max(colnames.index(c) for c in cols) >= 12 #Do we need any higher columns? +del out_fmt + +for in_file in args: + if not os.path.isfile(in_file): + stop_err("Input BLAST XML file not found: %s" % in_file) + + +re_default_query_id = re.compile("^Query_\d+$") +assert re_default_query_id.match("Query_101") +assert not re_default_query_id.match("Query_101a") +assert not re_default_query_id.match("MyQuery_101") +re_default_subject_id = re.compile("^Subject_\d+$") +assert re_default_subject_id.match("Subject_1") +assert not re_default_subject_id.match("Subject_") +assert not re_default_subject_id.match("Subject_12a") +assert not re_default_subject_id.match("TheSubject_1") + + +def convert(blastxml_filename, output_handle): + blast_program = None + # get an iterable + try: + context = ElementTree.iterparse(blastxml_filename, events=("start", "end")) + except: + stop_err("Invalid data format.") + # turn it into an iterator + context = iter(context) + # get the root element + try: + event, root = context.next() + except: + stop_err( "Invalid data format." ) + for event, elem in context: + if event == "end" and elem.tag == "BlastOutput_program": + blast_program = elem.text + # for every tag + if event == "end" and elem.tag == "Iteration": + #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA + # sp|Q9BS26|ERP44_HUMAN + # Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1 + # 406 + # + # + #Or, from BLAST 2.2.24+ run online + # Query_1 + # Sample + # 516 + # ... + qseqid = elem.findtext("Iteration_query-ID") + if re_default_query_id.match(qseqid): + #Place holder ID, take the first word of the query definition + qseqid = elem.findtext("Iteration_query-def").split(None,1)[0] + qlen = int(elem.findtext("Iteration_query-len")) + + # for every within + for hit in elem.findall("Iteration_hits/Hit"): + #Expecting either this, + # gi|3024260|sp|P56514.1|OPSD_BUFBU + # RecName: Full=Rhodopsin + # P56514 + #or, + # Subject_1 + # gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus] + # Subject_1 + # + #apparently depending on the parse_deflines switch + # + #Or, with a local database not using -parse_seqids can get this, + # gnl|BL_ORD_ID|2 + # chrIII gi|240255695|ref|NC_003074.8| Arabidopsis thaliana chromosome 3, complete sequence + # 2 + sseqid = hit.findtext("Hit_id").split(None,1)[0] + hit_def = sseqid + " " + hit.findtext("Hit_def") + if re_default_subject_id.match(sseqid) \ + and sseqid == hit.findtext("Hit_accession"): + #Place holder ID, take the first word of the subject definition + hit_def = hit.findtext("Hit_def") + sseqid = hit_def.split(None,1)[0] + if sseqid.startswith("gnl|BL_ORD_ID|") \ + and sseqid == "gnl|BL_ORD_ID|" + hit.findtext("Hit_accession"): + #Alternative place holder ID, again take the first word of hit_def + hit_def = hit.findtext("Hit_def") + sseqid = hit_def.split(None,1)[0] + # for every within + for hsp in hit.findall("Hit_hsps/Hsp"): + nident = hsp.findtext("Hsp_identity") + length = hsp.findtext("Hsp_align-len") + pident = "%0.2f" % (100*float(nident)/float(length)) + + q_seq = hsp.findtext("Hsp_qseq") + h_seq = hsp.findtext("Hsp_hseq") + m_seq = hsp.findtext("Hsp_midline") + assert len(q_seq) == len(h_seq) == len(m_seq) == int(length) + gapopen = str(len(q_seq.replace('-', ' ').split())-1 + \ + len(h_seq.replace('-', ' ').split())-1) + + mismatch = m_seq.count(' ') + m_seq.count('+') \ + - q_seq.count('-') - h_seq.count('-') + #TODO - Remove this alternative mismatch calculation and test + #once satisifed there are no problems + expected_mismatch = len(q_seq) \ + - sum(1 for q,h in zip(q_seq, h_seq) \ + if q == h or q == "-" or h == "-") + xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X") + if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx): + stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \ + % (qseqid, sseqid, expected_mismatch - q_seq.count("X"), + int(mismatch), expected_mismatch)) + + #TODO - Remove this alternative identity calculation and test + #once satisifed there are no problems + expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h) + if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")): + stop_err("%s vs %s identities, expected %i <= %i <= %i" \ + % (qseqid, sseqid, expected_identity, int(nident), + expected_identity + q_seq.count("X"))) + + + evalue = hsp.findtext("Hsp_evalue") + if evalue == "0": + evalue = "0.0" + else: + evalue = "%0.0e" % float(evalue) + + bitscore = float(hsp.findtext("Hsp_bit-score")) + if bitscore < 100: + #Seems to show one decimal place for lower scores + bitscore = "%0.1f" % bitscore + else: + #Note BLAST does not round to nearest int, it truncates + bitscore = "%i" % bitscore + + values = [qseqid, + sseqid, + pident, + length, #hsp.findtext("Hsp_align-len") + str(mismatch), + gapopen, + hsp.findtext("Hsp_query-from"), #qstart, + hsp.findtext("Hsp_query-to"), #qend, + hsp.findtext("Hsp_hit-from"), #sstart, + hsp.findtext("Hsp_hit-to"), #send, + evalue, #hsp.findtext("Hsp_evalue") in scientific notation + bitscore, #hsp.findtext("Hsp_bit-score") rounded + ] + + if extended: + try: + sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(" >")) + salltitles = "<>".join(name.split(None,1)[1] for name in hit_def.split(" >")) + except IndexError as e: + stop_err("Problem splitting multuple hits?\n%r\n--> %s" % (hit_def, e)) + #print hit_def, "-->", sallseqid + positive = hsp.findtext("Hsp_positive") + ppos = "%0.2f" % (100*float(positive)/float(length)) + qframe = hsp.findtext("Hsp_query-frame") + sframe = hsp.findtext("Hsp_hit-frame") + if blast_program == "blastp": + #Probably a bug in BLASTP that they use 0 or 1 depending on format + if qframe == "0": qframe = "1" + if sframe == "0": sframe = "1" + slen = int(hit.findtext("Hit_len")) + values.extend([sallseqid, + hsp.findtext("Hsp_score"), #score, + nident, + positive, + hsp.findtext("Hsp_gaps"), #gaps, + ppos, + qframe, + sframe, + #NOTE - for blastp, XML shows original seq, tabular uses XXX masking + q_seq, + h_seq, + str(qlen), + str(slen), + salltitles, + ]) + if cols: + #Only a subset of the columns are needed + values = [values[colnames.index(c)] for c in cols] + #print "\t".join(values) + output_handle.write("\t".join(values) + "\n") + # prevents ElementTree from growing large datastructure + root.clear() + elem.clear() + + +if options.output: + outfile = open(options.output, "w") +else: + outfile = sys.stdout + +for in_file in args: + blast_program = None + convert(in_file, outfile) + +if options.output: + outfile.close() +else: + #Using stdout + pass + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/blastxml_to_tabular.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,215 @@ + + Convert BLAST XML output to tabular + blastxml_to_tabular.py --version + +blastxml_to_tabular.py -o "$tabular_file" +#if $output.out_format == "cols": +#set cols = (str($output.std_cols)+","+str($output.ext_cols)).replace("None", " ").replace(",,", ",").replace(",", " ") +-c "$cols" +#else +-c "$output.out_format" +#end if +#for i in $blastxml_file#"${i}" #end for# + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of +formats including tabular and a more detailed XML format. A complex workflow +may need both the XML and the tabular output - but running BLAST twice is +slow and wasteful. + +This tool takes the BLAST XML output and can convert it into the +standard 12 column tabular equivalent: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 25 column tabular +BLAST output. This tool now uses this extended 25 column output by default. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length + 25 salltitles All subject title(s), separated by a '<>' +====== ============= =========================================== + +Beware that the XML file (and thus the conversion) and the tabular output +direct from BLAST+ may differ in the presence of XXXX masking on regions +low complexity (columns 21 and 22), and thus also calculated figures like +the percentage identity (column 3). + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + + + 10.7717/peerj.167 + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/check_no_duplicates.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/check_no_duplicates.py Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,46 @@ +#!/usr/bin/env python +"""Check for duplicate sequence identifiers in FASTA files. + +This is run as a pre-check before makeblastdb, in order to avoid +a regression bug in BLAST+ 2.2.28 which fails to catch this. See: +http://blastedbio.blogspot.co.uk/2012/10/my-ids-not-good-enough-for-ncbi-blast.html + +This script takes one or more FASTA filenames as input, and +will return a non-zero error if any duplicate identifiers +are found. +""" +import sys +import os + +if "-v" in sys.argv or "--version" in sys.argv: + print("v0.0.22") + sys.exit(0) + +def stop_err(msg, error=1): + sys.stderr.write("%s\n" % msg) + sys.exit(error) + + +identifiers = set() +files = 0 +for filename in sys.argv[1:]: + if not os.path.isfile(filename): + stop_err("Missing FASTA file %r" % filename, 2) + files += 1 + handle = open(filename) + for line in handle: + if line.startswith(">"): + #The split will also take care of the new line character, + #e.g. ">test\n" and ">test description here\n" both give "test" + seq_id = line[1:].split(None, 1)[0] + if seq_id in identifiers: + handle.close() + stop_err("Repeated identifiers, e.g. %r" % seq_id, 1) + identifiers.add(seq_id) + handle.close() +if not files: + stop_err("No FASTA files given to check for duplicates", 3) +elif files == 1: + print("%i sequences" % len(identifiers)) +else: + print("%i sequences in %i FASTA files" % (len(identifiers), files)) diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,48 @@ + + Show BLAST database information from blastdbcmd + + blastdbcmd + ncbi_macros.xml + + + +blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info" + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Calls the NCBI BLAST+ blastdbcmd command line tool with the -info +switch to give summary information about a BLAST database, such as +the size (number of sequences and total length) and date. + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,118 @@ + + Extract sequence(s) from BLAST database + + blastdbcmd + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" + +##TODO: What about -ctrl_a and -target_only as advanced options? + +#if $id_opts.id_type=="file": +-entry_batch "$id_opts.entries" +#else: +##Perform some simple search/replaces to remove whitespace +##and make it comma separated, and escape any pipe characters +-entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',').replace('|','\|')" +#end if + +##When building a BLAST database, to ensure unique IDs makeblastdb will +##do things like turning a FASTA entry with ID of ERP44 into lcl|ERP44 +##(if using -parse_seqids) or simply assign it an ID using the record +##number like gnl|BL_ORD_ID|123 (to cope with duplicate IDs in the FASTA +##file). In -parse_seqids mode, a duplicate FASTA ID gives an error. +## +##The BLAST plain text and XML output will contain these BLAST IDs, but +##the tabular output does not (at least, not in BLAST 2.2.25+). +##Therefore in general, Galaxy users won't care about the (internal) +##BLAST identifiers. +## +##The blastdbcmd FASTA output will also contain these IDs, but in the +##context of the BLAST tabular output they are not helpful. Therefore +##to recover the original ID as used in the FASTA file for makeblastdb +##we need a litte post processing. +## +##We remove the NCBI's lcl|... or gnl|BL_ORD_ID|123 prefixes +##using sed, however the exact syntax differs for Mac OS X's sed + +#if str($outfmt)=="blastid": +-out "$seq" +#else if sys.platform == "darwin": +| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq" +#else: +| sed 's/>$lcl|\|gnl|BL_ORD_ID|[0-9]* $/>/1' > "$seq" +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Extracts FASTA formatted sequences from a BLAST database +using the NCBI BLAST+ blastdbcmd command line tool. + +.. class:: warningmark + +**BLAST assigned identifiers** + +When a BLAST database is constructed from a FASTA file, the +original identifiers can be replaced with BLAST assigned +identifiers, partly to ensure uniqueness. e.g. Sometimes +a prefix of 'lcl|' is added (lcl is short for local), +or an arbitrary name starting 'gnl|BL_ORD_ID|' is created. + +If you are using the tabular output from BLAST, it will contain +the original identifiers - not the BLAST assigned identifiers +suitable for use with the blastdbcmd tool. + +If you are using the XML or plain text output, this will also +contain the BLAST assigned identifiers. However, this means +getting a list of BLAST assigned identifiers isn't straightforward. + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,156 @@ + + Search nucleotide database with nucleotide query sequence(s) + + + + blastn + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastn +-query "$query" +@BLAST_DB_SUBJECT@ +-task $blast_type +-evalue $evalue_cutoff +@BLAST_OUTPUT@ +@THREADS@ +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.strand +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ +#if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): +-perc_identity $adv_opts.identity_cutoff +#end if +$adv_opts.ungapped +@ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ +## End of advanced options: +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@SEARCH_TIME_WARNING@ + +**What it does** + +Search a *nucleotide database* using a *nucleotide query*, +using the NCBI BLAST+ blastn command line tool. +Algorithms include blastn, megablast, and discontiguous megablast. + +@FASTA_WARNING@ + +----- + +@OUTPUT_FORMAT@ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,158 @@ + + Search protein database with protein query sequence(s) + + + + blastp + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastp +-query "$query" +@BLAST_DB_SUBJECT@ +-task $blast_type +-evalue $evalue_cutoff +@BLAST_OUTPUT@ +@THREADS@ +#if $adv_opts.adv_opts_selector=="advanced": +-matrix $adv_opts.matrix +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped +@ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ +## End of advanced options: +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@SEARCH_TIME_WARNING@ + +**What it does** + +Search a *protein database* using a *protein query*, +using the NCBI BLAST+ blastp command line tool. + +@FASTA_WARNING@ + +----- + +@OUTPUT_FORMAT@ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,138 @@ + + Search protein database with translated nucleotide query sequence(s) + + + + blastx + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastx +-query "$query" +@BLAST_DB_SUBJECT@ +-query_gencode $query_gencode +-task $blast_type +-evalue $evalue_cutoff +@BLAST_OUTPUT@ +@THREADS@ +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.strand +-matrix $adv_opts.matrix +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ +$adv_opts.ungapped +@ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ +## End of advanced options: +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@SEARCH_TIME_WARNING@ + +**What it does** + +Search a *protein database* using a *translated nucleotide query*, +using the NCBI BLAST+ blastx command line tool. + +@FASTA_WARNING@ + +----- + +@OUTPUT_FORMAT@ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,88 @@ + + Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb + + convert2blastmask + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +convert2blastmask +-in $infile +-masking_algorithm "$masking_algorithm" +-masking_options "$masking_options" +$parse_seqids +-out "$outfile" +-outfmt $outformat + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb. + +More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_. + +.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,100 @@ + + + masks low complexity regions + + dustmasker + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +dustmasker +#if $db_opts.db_opts_selector == "db": + -in "${db_opts.database.fields.path}" -infmt blastdb +#elif $db_opts.db_opts_selector == "histdb": + -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb +#else: + -in "$subject" -infmt fasta +#end if +-out "$outfile" +-window $window -level $level -linker $linker -outfmt $outformat + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST_ algorithm. + +If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. + +More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. + +.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549 + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,504 @@ + + + + @BINARY@ + blast+ + + @BINARY@ -version + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +#if float(str($adv_opts.qcov_hsp_perc)) > 0: + -qcov_hsp_perc $adv_opts.qcov_hsp_perc +#end if + + +#if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist': + -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist +#elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist': + -gilist $adv_opts.adv_optional_id_files_opts.gilist +#elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist': + -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist +#end if + + -num_threads "\${GALAXY_SLOTS:-8}" + +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#elif $db_opts.db_opts_selector == "histdb": + -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" +#else: + -subject "$db_opts.subject" +#end if + + -out "$output1" +##Set the extended list here so when we add things, saved workflows are not affected +#if str($output.out_format)=="ext": + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles" +#elif str($output.out_format)=="cols" +##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated: +##TODO - Can we catch the user picking no columns and raise an error here? +#set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip() + -outfmt "6 $cols" +#else: + -outfmt $output.out_format +#end if + + $adv_opts.filter_query + +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments +## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI) +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +#if str($output.out_format) in ["6", "ext", "cols", "5"]: +## Most output formats use this, including tabular and XML: +-max_target_seqs $adv_opts.max_hits +#else +## Text and HTML output formats 0-4 currently need this instead: +-num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits +#end if +#end if + + +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if +$adv_opts.parse_deflines + + + #if str($db_opts.db_opts_selector)=='db' +${db_opts.database} +#elif str($db_opts.db_opts_selector)=='histdb' +${db_opts.histdb.name} +#else +${db_opts.subject.name} +#end if + +Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). +NCBI BLAST+ integrated into Galaxy. *BioRxiv* preprint. +http://dx.doi.org/10.1101/014043 + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. *PeerJ* 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +*BMC Bioinformatics*. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + + + + 10.1186/1471-2105-10-421 + 10.7717/peerj.167 + + 10.1101/014043 + + + + **Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Many commonly used extra columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 25 column tabular +BLAST output. Galaxy now uses this extended 25 column output by default. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length + 25 salltitles All subject title(s), separated by a '<>' +====== ============= =========================================== + +The third option is to customise the tabular output by selecting which +columns you want, from the standard set of 12, the default set of 25, +or any of the additional columns BLAST+ offers (including species name). + +The fourth option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + + .. class:: warningmark + +You can also search against a FASTA file of subject (target) +sequences. This is *not* advised because it is slower (only one +CPU is used), but more importantly gives e-values for pairwise +searches (very small e-values which will look overly signficiant). +In most cases you should instead turn the other FASTA file into a +database first using *makeblastdb* and search against that. + + .. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,204 @@ + + Make BLAST database + + makeblastdb + ncbi_macros.xml + + + check_no_duplicates.py +##First check for duplicates (since BLAST+ 2.2.28 fails to do so) +##and abort (via the ampersand ampersand trick) if any are found. +#for i in $input_file#"${i}" #end for# +&& +makeblastdb -out "${os.path.join($outfile.files_path,'blastdb')}" +$parse_seqids +$hash_index +## Single call to -in with multiple filenames space separated with outer quotes +## (presumably any filenames with spaces would be a problem). Note this gives +## some extra spaces, e.g. -in "file1 file2 file3 " but BLAST seems happy: +-in "#for i in $input_file#${i} #end for#" +#if $title: +-title "$title" +#else: +##Would default to being based on the cryptic Galaxy filenames, which is unhelpful +-title "BLAST Database" +#end if +-dbtype $dbtype +## -------------------------------------------------------------------- +## Masking +## -------------------------------------------------------------------- +## HACK: If no mask files, evaluates as a list with just None in it: +## See Trello issue https://trello.com/c/lp5YmA1O +#if ' '.join( map(str, $mask_data_file) ) != 'None': +#for i in $mask_data_file: +-mask_data "${i}" +#end for +#end if +## -------------------------------------------------------------------- +## Taxonomy +## -------------------------------------------------------------------- +#if $tax.taxselect == 'id': +-taxid $tax.taxid +## TODO - Can we use a tabular file for the taxonomy mapping? +## #else if $tax.taxselect == 'map': +## -taxid_map $tax.taxmap +#end if +## -------------------------------------------------------------------- +## Capture the stdout log information to the primary file (plain text): +> "$outfile" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Make BLAST database from one or more FASTA files and/or BLAST databases. + +This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the +replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite. + + + +**Documentation** + +http://www.ncbi.nlm.nih.gov/books/NBK1763/ + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,128 @@ + + Make profile database + + makeprofiledb + ncbi_macros.xml + + + +##Unlike makeblastdb, makeprofiledb needs directory to exist already: +mkdir -p $outfile.files_path && +makeprofiledb -out "${os.path.join($outfile.files_path,'blastdb')}" + +##We turn $infile_list into $infiles with a configfile entry defined below +-in $infiles + +#if $title: +-title "$title" +#else: +##Would default to being based on the cryptic Galaxy filenames, which is unhelpful +-title "Profile Database" +#end if + +-threshold $threshold + +#if str($contain_pssm_scores.contain_pssm_scores_type) == 'no': + -gapopen $contain_pssm_scores.gapopen + -gapextend $contain_pssm_scores.gapextend + -scale $contain_pssm_scores.scale + -matrix $contain_pssm_scores.matrix +#end if + +-obsr_threshold $obsr_threshold +-exclude_invalid $exclude_invalid + +-logfile "$outfile" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +#for $infile in $input_file +${infile} +#end for + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Make a protein domain profile database (for use with RPS-BLAST or RSP-TBLASTN) +from one or more Position Specific Scoring Matrices (PSSM) files in the NCBI +"scoremat" ASN.1 format (usually named ``*.smp``). + +This is a wrapper for the NCBI BLAST+ tool 'makeprofiledb'. + +More information about makeprofiledb can be found in the `BLAST Command Line Applications User Manual`_. + +.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ + + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,120 @@ + + Search protein domain database (PSSMs) with protein query sequence(s) + + + + deltablast + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +rpsblast +-query "$query" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#elif $db_opts.db_opts_selector == "histdb": + -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" +#end if +-evalue $evalue_cutoff +@BLAST_OUTPUT@ +@THREADS@ +#if $adv_opts.adv_opts_selector=="advanced": +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_QCOV_HSP_PERC@ +## End of advanced options: +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@SEARCH_TIME_WARNING@ + +**What it does** + +Search a *protein domain database* using a *protein query*, +using the NCBI BLAST+ rpsblast command line tool. + +The protein domain databases use position-specific scoring matrices +(PSSMs) and are available for a number of domain collections including: + +*CDD* - NCBI curarated meta-collection of domains, see +http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains + +*Kog* - PSSMs from automatically aligned sequences and sequence +fragments classified in the KOGs resource, the eukaryotic +counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/ + +*Cog* - PSSMs from automatically aligned sequences and sequence +fragments classified in the COGs resource, which focuses primarily +on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ + +*Pfam* - PSSMs from Pfam-A seed alignment database, see +http://pfam.sanger.ac.uk/ + +*Smart* - PSSMs from SMART domain alignment database, see +http://smart.embl-heidelberg.de/ + +*Tigr* - PSSMs from TIGRFAM database of protein families, see +http://www.jcvi.org/cms/research/projects/tigrfams/overview/ + +*Prk* - PSSms from automatically aligned stable clusters in the +Protein Clusters database, see +http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters + +The exact list of domain databases offered will depend on how your +local Galaxy has been configured. + +----- + +@OUTPUT_FORMAT@ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,118 @@ + + Search protein domain database (PSSMs) with translated nucleotide query sequence(s) + + + + rpstblastn + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +rpstblastn +-query "$query" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#elif $db_opts.db_opts_selector == "histdb": + -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" +#end if +-evalue $evalue_cutoff +@BLAST_OUTPUT@ +## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+. +##-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_QCOV_HSP_PERC@ +## End of advanced options: +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@SEARCH_TIME_WARNING@ + +**What it does** + +Search a *protein domain database* using a *nucleotide query*, +using the NCBI BLAST+ rpstblastn command line tool. + +The protein domain databases use position-specific scoring matrices +(PSSMs) and are available for a number of domain collections including: + +*CDD* - NCBI curarated meta-collection of domains, see +http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains + +*Kog* - PSSMs from automatically aligned sequences and sequence +fragments classified in the KOGs resource, the eukaryotic +counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/ + +*Cog* - PSSMs from automatically aligned sequences and sequence +fragments classified in the COGs resource, which focuses primarily +on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ + +*Pfam* - PSSMs from Pfam-A seed alignment database, see +http://pfam.sanger.ac.uk/ + +*Smart* - PSSMs from SMART domain alignment database, see +http://smart.embl-heidelberg.de/ + +*Tigr* - PSSMs from TIGRFAM database of protein families, see +http://www.jcvi.org/cms/research/projects/tigrfams/overview/ + +*Prk* - PSSms from automatically aligned stable clusters in the +Protein Clusters database, see +http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters + +The exact list of domain databases offered will depend on how your +local Galaxy has been configured. + +----- + +@OUTPUT_FORMAT@ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,102 @@ + + low-complexity regions in protein sequences + + segmasker + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +segmasker +#if $db_opts.db_opts_selector == "db": + -in "${db_opts.database.fields.path}" -infmt blastdb +#elif $db_opts.db_opts_selector == "histdb": + -in "${os.path.join($db_opts.histdb.files_path, 'blastdb')}" -infmt blastdb +#else: + -in "$subject" -infmt fasta +#end if +-out "$outfile" +-window $window +-locut $locut +-hicut $hicut +-outfmt $outformat + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool identifies and masks out low complexity regions of a protein database (or proteins in FASTA format) by using the SEG_ algorithm. + +If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. + +More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_. + +.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ +.. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706 + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,173 @@ + + Search translated nucleotide database with protein query sequence(s) + + + + tblastn + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastn +-query "$query" +@BLAST_DB_SUBJECT@ +-task $blast_type +-evalue $evalue_cutoff +@BLAST_OUTPUT@ +@THREADS@ +#if $adv_opts.adv_opts_selector=="advanced": +-db_gencode $adv_opts.db_gencode +-matrix $adv_opts.matrix +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped +@ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ +## End of advanced options: +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@SEARCH_TIME_WARNING@ + +**What it does** + +Search a *translated nucleotide database* using a *protein query*, +using the NCBI BLAST+ tblastn command line tool. + +@FASTA_WARNING@ + +----- + +@OUTPUT_FORMAT@ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,100 @@ + + Search translated nucleotide database with translated nucleotide query sequence(s) + + + + tblastx + ncbi_macros.xml + + + +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastx +-query "$query" +@BLAST_DB_SUBJECT@ +-query_gencode $query_gencode +-evalue $evalue_cutoff +@BLAST_OUTPUT@ +@THREADS@ +#if $adv_opts.adv_opts_selector=="advanced": +-db_gencode $adv_opts.db_gencode +$adv_opts.strand +-matrix $adv_opts.matrix +@ADV_FILTER_QUERY@ +@ADV_MAX_HITS@ +@ADV_WORD_SIZE@ +@ADV_ID_LIST_FILTER@ +@ADV_QCOV_HSP_PERC@ +## End of advanced options: +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +@SEARCH_TIME_WARNING@ + +**What it does** + +Search a *translated nucleotide database* using a *translated nucleotide query*, +using the NCBI BLAST+ tblastx command line tool. + +@FASTA_WARNING@ + +----- + +@OUTPUT_FORMAT@ + +------- + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +@REFERENCES@ + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,4 @@ + + + + diff -r 000000000000 -r 432ea9614cc9 tools/ncbi_blast_plus/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Fri Jan 30 08:27:28 2015 -0500 @@ -0,0 +1,6 @@ + + + + + +