# HG changeset patch # User peterjc # Date 1478536183 18000 # Node ID d8f2c1f560ec7817447cb1c8ef03c9ea04bb9366 # Parent 4c47abb4c993937d699fc0e92e95cf528d9c8de0 Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes. diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_bufo.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rhodopsin_bufo.fasta Mon Nov 07 11:29:43 2016 -0500 @@ -0,0 +1,21 @@ +>gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete cds +TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCCAAACTTTTACATACCCATG +TCCAACAAGACTGGGGTGGTGCGAAGCCCCTTTGAATACCCTCAGTATTACCTGGCAGAGCCATGGCAATATTCCATTCT +GTGCGCGTACATGTTCCTGCTCATTCTACTTGGGTTCCCAATCAACTTCATGACCTTGTACGTCACCATCCAGCACAAGA +AGCTCCGGACACCCTTAAACTATATCCTGCTGAATTTGGCCTTTGCCAACCACTTCATGGTCCTGTGTGGATTCACGGTG +ACAATGTACTCCTCAATGAACGGATACTTCATCCTCGGAGCCACCGGTTGCTATGTTGAAGGCTTCTTCGCTACCCTTGG +TGGTGAAATCGCCCTTTGGTCCCTGGTGGTCTTGGCCATTGAACGATACGTGGTCGTCTGTAAGCCCATGAGCAACTTCC +GATTTAGTGAGAACCATGCCGTCATGGGCGTAGCGTTCACCTGGATAATGGCTTTGTCCTGTGCTGTTCCTCCACTCCTT +GGATGGTCCAGGTACATCCCCGAGGGCATGCAGTGCTCCTGCGGAGTCGACTACTACACCCTGAAGCCCGAGGTCAACAA +CGAGTCCTTCGTCATCTACATGTTCGTCGTCCACTTCACCATCCCCCTGATTATCATTTTCTTCTGCTATGGCCGCCTGG +TGTGCACTGTGAAAGAGGCTGCAGCTCAACAGCAAGAGTCCGCCACCACCCAGAAGGCCGAGAAAGAGGTGACCAGGATG +GTGATCATCATGGTGGTCTTCTTCCTTATCTGTTGGGTCCCCTACGCCTCTGTCGCTTTCTTCATCTTCAGCAATCAGGG +CTCTGAGTTCGGCCCCATCTTCATGACCGTCCCAGCTTTCTTTGCCAAGAGTTCTTCCATCTACAACCCCGTCATCTACA +TCATGCTCAACAAGCAGTTCCGTAACTGCATGATCACCACCCTGTGCTGCGGCAAGAATCCCTTTGGAGAAGACGATGCC +TCCTCTGCCGCCACCTCCAAGACAGAGGCTTCTTCTGTTTCTTCCAGCCAGGTGTCTCCTGCATAAGACCTTCCACCAGG +CCTGTCTCAGGGTCCGCTGCCTCACACAGCTCCCACCGCCCCAACTCCGTCTCCTGCTCGCTAAGGCGGCGAAGTTCCCC +TTCCATTACATAAAACGTATCTGTTCAAGAAAGGCGACGACGAAGGAGAAGAAGAGGAGCCCCCCCGAACCCCTTCGCTG +CTGCTGAAAACGACTTGATTGCTTCTGCAACGCAACGGGGCCTTACGGCAGCGAAGGGGTTGTCATCCGGACGCGCCAAG +AATTCCTTCGAGACTGTAAATATCTTAAAGGAACCGTCCTGCTAGTTACCGACGCCGCTCCTGTAGCCGCCGTTCCCCCG +CACTCCGGCCGGTTCATACCTCTTATTTTTTTGCAATGCAACAGAAAATAATATTTTTGTTCCCACGGCTTTTCCCGGTC +AGGTCTGGTAGTGGCGGAGATTGGCCGACCCCTCGCACCTGTAATAAAGCGCAG diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.dbinfo.txt --- a/test-data/rhodopsin_nucs.dbinfo.txt Wed Mar 09 06:13:17 2016 -0500 +++ b/test-data/rhodopsin_nucs.dbinfo.txt Mon Nov 07 11:29:43 2016 -0500 @@ -1,7 +1,7 @@ Database: Rhodopsin nucleotides 6 sequences; 10,296 total bases -Date: Mar 8, 2016 4:58 PM Longest sequence: 4,301 bases +Date: Oct 14, 2016 2:16 PM Longest sequence: 4,301 bases Volumes: /mnt/galaxy/repositories/galaxy_blast/test-data/rhodopsin_nucs.fasta diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta --- a/test-data/rhodopsin_nucs.fasta Wed Mar 09 06:13:17 2016 -0500 +++ b/test-data/rhodopsin_nucs.fasta Mon Nov 07 11:29:43 2016 -0500 @@ -1,161 +1,138 @@ >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 - +ATGAACGGGACGGAGGGCCCGAACTTCTACGTGCCCTTCTCCAACAAAACGGGTGTGGTACGCAGCCCCTTCGAGTACCC +ACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTCCTGCTCATCGTGCTTGGCTTCCCCA +TCAACTTCCTCACGCTCTACGTCACGGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCC +GTGGCTGACCTCTTCATGGTCTTCGGTGGCTTCACCACCACCCTCTACACCTCTCTGCATGGATACTTTGTCTTTGGGCC +CACAGGATGCAATTTGGAGGGCTTCTTTGCCACACTGGGCGGTGAAATTGCCCTGTGGTCTTTGGTGGTCCTGGCCATTG +AGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTTGGGGAGAACCATGCCATAATGGGCGTCGCTTTCACC +TGGGTCATGGCACTGGCCTGCGCTGCACCCCCCCTCGTTGGTTGGTCCAGGTACATCCCTGAAGGCATGCAGTGTTCATG +CGGGATCGACTACTACACACTCAAGCCAGAAGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACTTCACCA +TCCCCATGATCGTCATCTTCTTTTGCTACGGGCAGCTTGTCTTCACAGTCAAGGAGGCGGCAGCCCAGCAGCAGGAGTCA +GCCACCACCCAGAAGGCTGAGAAGGAGGTCACTCGCATGGTCATCATCATGGTCATTGCTTTCCTGATCTGTTGGGTGCC +CTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGGTCCAACTTTGGCCCCATCTTCATGACACTCCCGGCGTTCT +TCGCAAAGTCCTCCTCCATCTACAACCCTGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACTACC +CTCTGCTGTGGCAAGAACCCACTGGGTGATGACGAGGCTTCCACAACCGGTTCCAAGACGGAGACCAGCCAGGTGGCACC +GGCCTAA >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 - +TCTTTCTAGTTTGGGGGGGGGGACTTTAAAGAGCCGCCAATATGAACGGAACAGAAGGCCCAAACTTTTACATACCCATG +TCCAACAAGACTGGGGTGGTGCGAAGCCCCTTTGAATACCCTCAGTATTACCTGGCAGAGCCATGGCAATATTCCATTCT +GTGCGCGTACATGTTCCTGCTCATTCTACTTGGGTTCCCAATCAACTTCATGACCTTGTACGTCACCATCCAGCACAAGA +AGCTCCGGACACCCTTAAACTATATCCTGCTGAATTTGGCCTTTGCCAACCACTTCATGGTCCTGTGTGGATTCACGGTG +ACAATGTACTCCTCAATGAACGGATACTTCATCCTCGGAGCCACCGGTTGCTATGTTGAAGGCTTCTTCGCTACCCTTGG +TGGTGAAATCGCCCTTTGGTCCCTGGTGGTCTTGGCCATTGAACGATACGTGGTCGTCTGTAAGCCCATGAGCAACTTCC +GATTTAGTGAGAACCATGCCGTCATGGGCGTAGCGTTCACCTGGATAATGGCTTTGTCCTGTGCTGTTCCTCCACTCCTT +GGATGGTCCAGGTACATCCCCGAGGGCATGCAGTGCTCCTGCGGAGTCGACTACTACACCCTGAAGCCCGAGGTCAACAA +CGAGTCCTTCGTCATCTACATGTTCGTCGTCCACTTCACCATCCCCCTGATTATCATTTTCTTCTGCTATGGCCGCCTGG +TGTGCACTGTGAAAGAGGCTGCAGCTCAACAGCAAGAGTCCGCCACCACCCAGAAGGCCGAGAAAGAGGTGACCAGGATG +GTGATCATCATGGTGGTCTTCTTCCTTATCTGTTGGGTCCCCTACGCCTCTGTCGCTTTCTTCATCTTCAGCAATCAGGG +CTCTGAGTTCGGCCCCATCTTCATGACCGTCCCAGCTTTCTTTGCCAAGAGTTCTTCCATCTACAACCCCGTCATCTACA +TCATGCTCAACAAGCAGTTCCGTAACTGCATGATCACCACCCTGTGCTGCGGCAAGAATCCCTTTGGAGAAGACGATGCC +TCCTCTGCCGCCACCTCCAAGACAGAGGCTTCTTCTGTTTCTTCCAGCCAGGTGTCTCCTGCATAAGACCTTCCACCAGG +CCTGTCTCAGGGTCCGCTGCCTCACACAGCTCCCACCGCCCCAACTCCGTCTCCTGCTCGCTAAGGCGGCGAAGTTCCCC +TTCCATTACATAAAACGTATCTGTTCAAGAAAGGCGACGACGAAGGAGAAGAAGAGGAGCCCCCCCGAACCCCTTCGCTG +CTGCTGAAAACGACTTGATTGCTTCTGCAACGCAACGGGGCCTTACGGCAGCGAAGGGGTTGTCATCCGGACGCGCCAAG +AATTCCTTCGAGACTGTAAATATCTTAAAGGAACCGTCCTGCTAGTTACCGACGCCGCTCCTGTAGCCGCCGTTCCCCCG +CACTCCGGCCGGTTCATACCTCTTATTTTTTTGCAATGCAACAGAAAATAATATTTTTGTTCCCACGGCTTTTCCCGGTC +AGGTCTGGTAGTGGCGGAGATTGGCCGACCCCTCGCACCTGTAATAAAGCGCAG >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 - +GTGCCCTTCTCCAACAAGACAGGCGTGGTGCGCAGTCCCTTCGAGCATCCACAGTACTACCTGGCCGAGCCATGGCAGTT +CTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTCGGCTTCCCCATCAACTTCCTCACGCTCTATGTCACGGTTC +AGCACAAGAAGCTGCGTACGCCTCTCAACTACATCCTGCTCAACCTGGCCGTGGCCGACCTCTTCATGGTCTTCGGAGGC +TTCACCACCACCCTCTACACCTCCCTGCATGGATACTTTGTCTTCGGGCCTACGGGATGCAATCTGGAGGGCTTTTTTGC +CACCCTGGGAGGTATGAGCTGAGATGCGGGTAAGGAGGAGGCATAGAGGCATCTGGGAACAGTCCCAAGCTTGGGGTGAA +GGCTAAGAGGCCTTCTTCCTTGTTCTGTCATTGGCGTCGTCCGAAGCCCTCACTTAATCAACAAACAGTTTGGTGGTGAG +GCGCTGAGCTCCATTTGGAGAGGGCAGGTATCGAGCACTGTTTTATCCCCCCTGGAGTGGTGCCATTGCCTTGCTTTACA +GCAAAGAAACTGAGGATGAGAGGAGTCGAGGGTCTTGCCAGGTCACATCATGGCAGAGACAGAGCTGAGTTTCAACCCTG +CATCTATGTGCAGTTTCCCTTGGAGCAGCTATGTTAGGTCAGACCCACGGTGGGCACTGGGGAGAGAGCTGCACAAGACA +GGTCCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNTTCCTGATTGCCAGGAGTGATGTGCAGCGCAAATGTCTGAATTCCATTATTAT +GTGCTCCTTCTTCCTCTGAGCCAAACATCCATCTTCATGGCTCCTAGAATTGGGTCCCACCCACATGAGCAGGTCATTTT +GTTTCCCTAGAGGGGAGAGGTCACTGCTGTGGAGGGAGGGAAGGTTCGTCCCGCTCCATGTTTCTGTTGTCTCTGCAATG +CCTTTCTCTAGGGACTCTGCCTATTGCCCCAAGAAGGACACATTCTTCTGTAAAAACTCCCTCCTGGGTTCCCAGTCTAA +TCAAGACCTCTAAACTGATTTCCATGTCCCTCATGAACCCAAAGCTCTAACTGAATTAAACTTCTCAGGACTTACTCCAC +TCTCCTCGTCCATCATGCAGCCCCTCTGCCCAGCACCCTATCTCCTCTTCTTCCCAGTGTCTGAGCCCACTGTACCCTGA +GACTTCGCTCCAGGCCTGCCCCAGGCTGCCTTCTCAGGTGCCCTCTCCCACATAGGAGGAGCACGGCCTCCTTAGACAGA +CGTGGGGTGCAGGTTGGTGGCATGCTGACTGATAGCTGACTGCCTTGCAGGTGAAATTGCCCTGTGGTCCTTGGTGGTCC +TGGCCATCGAGCGGTACGTGGTGGTATGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCCTT +GCCCTCACCTGGGTCATGGCACTGGCCTGCGCCGCGCCCCCGCTAGTCGGCTGGTCCAGGTAATGGCACTGAACAGAAGG +GAAGTGCCTCTGAGGTCTTCTTAGGGTCCCCCAGCTGGGACTCAAACCTAGGGCTGTCTGGTTCCAGGCACGGAACTGGC +GACTCCACTGGGGTTGGGGTTTAGGGCAAGGAAGGAGAGGATCAGACCCTAATGTTGTTACGTGGGTTGGTCCGCATGTC +AAGGAGAATCCAAGACACCCAATCCTTCACCTTGGCTGTGCCCCTAATCCTCATCTAAGCCAGGTTCAGATTCCAATCCT +CTTTGGCCCAGTGCTCCGTGGGAAGCTCCCTCTGACCTTGGGCCTCAGCGCCTGGGGTTGCTGAGCCTTCCTAGTATAGG +TGGTGACATCGTAGCCCCTGGGACCTGGATCCTGCCCAGTCTGCAGGCCATCATCTCCAAATGGGGCTGAGATGAGATGT +GAGGAAAGAGGGGAGACAGTGGTTTGGAAAACTGGACTGGTGGCTTTTTTGGGTTTCCAGAGGACTCATCTTCCTCTGCT +TCTAGAATATTCCCACTCTCTCTTCCCTTTCCTCATTCTTCCTGGGTTATTTTTTTTTCCCTTTGCTGAATTCGAGCCCC +ATTCCCTCCAGCCTCTTTCCCTGTCTTATCTAGCCCAGTCCAGTTATATTCTCATAGGCAGAGGCAACAGATGCTCCAAA +TTTTCTGAGGTCGGTTCCAACATCGCCACCCTCTAAAATCAGTGAAACATCCTAACTACATGCCTCATAGTCCTCCTGTT +TCCAAAAACTGCAAAGATCTCCTGGTTACCCTGTATGCCCATCTTTGGGCTAGAAAATCCTCTCACCCTGTTAATAGTAA +GACCCTGGTTTGTACAAACTGCCTCAAACACAGAGTTTAGGGGCTTTTCCCTTCTCTCCGCCAACCTCTGACAGGCAGAG +TCTGAGGCCTGGCCTCCAGCTGCTGCGGGGAGCAGGTCTGGTAAAGAATCCTGTGCAGGTCAGTGGTATACAGGTCCTGT +CAGGTGACAGCCTGGGCGAGAGACTGGAAAGTATCAGGATAACACGGCTGCCAGACGAACAACAAAACAACACTGAATTC +ACAAGGCGCATTCGAATCCTCTCTCAGTCCATTTGATCCTCAGTCACACAGCCGAGTAGACACTTTATCAACTCATTTAA +CAGAAAGGGAAAGTGAAGCCCAGAGCGAGGCCAGCAACGTGGCAGGTCACTCTGGTCATCTAGGGCCTGTTCCCAACTCT +TTCACATGTGGGTCTCCAATATGTTCCCTCCTGTCCCAATCTCTGCCGGCCCTCAGGTACATCCCAGAGGGCATGCAGTG +CTCATGTGGAATCGACTACTACACCCTCAAGCCGGAGGTCAACAACGAGTCCTTTGTCATCTACATGTTCGTGGTCCACT +TCACCATCCCTATGATTGTCATATTCTTTTGCTATGGACAGCTGGTCTTCACCGTCAAGGAGGTAAGGTCATGTGTTGGG +CACTGGGGACATGCACACTGAGTGAATGGAGCCCAGCTCCATTCCCAGAGTTGCCACAGTCTGGACACCTGACCTTGTGT +CCCTGCAGGCAGCTGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCCGAGAAGGAGGTCACCCGTATGGTCATCATC +ATGGTCATTGCTTTCCTAATCTGTTGGCTGCCGTATGCCGGCGTGGCATTCTACATCTTCACCCACCAGGGCTCTAACTT +TGGCCCCATCTTCATGACCCTCCCGGCATTCTTTGCCAAGTCGTCCTCCATCTACAACCCTGTCATCTATATCATGATGA +ACAAGCAGGTGCCAGGTGGTAGGGAGGGAGGGTCTGGGTCCCCCAGGCTGCAGGCACTGCCCACAGAGGACAAGCCACAT +CCTTGACTAGGCAGACCCCAGTCTTCCCATCTGCAAAATTAGGCAGGGGAGTTCGTCTCCCCCAGGCATCAGAGACATCG +GGGAGAAATGCACATTTCTGGAGATGAATCAGCATCTCAGGGTGGGCCCAGGAACCTGCACTTCTAAAAACCATTCCACA +TGACTCTGAGGCTAGCATGAGAAGTGATGATCCACATGGTTCTGGAGGCCTGCTTTAAAAGTCAAGTGGTCAAAGTCCCA +AGCCTGGGAACGGGATGGTGCCAGTCTCCATTAAAGAGATCAAAAGGAGCTAGAAAGTCTTGTGATGAAAGATGAAGGGA +TAAAGCCGTCCTTTAACACAGATCAGTGATTTCTCTGCAGAATCCATGACCCAGTGGGAAAAAGTGGTCCCTGGAGTCAG +GCATATTGGATTCAAATCCTAGCTCTGCTATTTTCTAGCTATGTAACCTTGGGCAAGTCATCTCCCTTCTCTGTGCTTCA +GTTTCTTCTTTCATAGAAAGGGTAAAATCCCAAACTCTTGGGTTAAATGAGATAACTTACATAGCCCTTGATATGCAGAG +GCATTATGGAATGTCGTTAGTGACAAAGTTCCCTTGGGTTTGGTCCCTGGTATCTCTGGAGTGAGATTGCATATGTTCCC +TTCAGAGGGTCAGATTTGGGATGAGAGTGGAGGCTGCGAGGGCCTGAGTGGGAAGGGATTGGAGGCAAATCTCACCAACC +ATGTCAGTTTGCTACACACACTTTGGGTGGACCCTGACCCTGACTCATGCTTCTTGCCTTCCAGTTCCGGAACTGCATGC +TCACTACCCTCTGCTGTGGCAAGAACCCACTGGGTGACGATGAGGCCTCCACCACTGCCTC >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 - +GTGCCCTTCTCCAACAAGACGGGTGTGGTGCGCAGCCCCTTCGAGTACCCGCAGTACTACCTGGCTGAGCCCTGGCAGTT +CTCCATGCTGGCTGCCTACATGTTTCTGCTGATCGTGCTCGGATTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCC +AGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTGGCTGTGGCCAACCTCTTCATGGTCTTTGGAGGC +TTCACCACCACCCTGTATACCTCTATGCATGGATACTTCGTCTTCGGGGCCACGGGATGCAATCTGGAGGGCTTCTTTGC +CACGCTGGGCGGTGAAATCGCCCTGTGGTCCCTGGTGGTCCTGGCCATCGAGCGGTATGTGGTGGTCTGCAAGCCCATGA +GCAACTTCCGCTTTGGGGAGAACCACGCCATCATGGGCCTCGCCTTCACGTGGGTCATGGCACTGGCCTGCGCTGCACCC +CCACTAGCCGGCTGGTCCAGGTACATCCCAGAGGGCATGCAGTGCTCGTGTGGGATTGACTACTACACGCTCAAACCGGA +GGTCAACAACGAGTCCTTCGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTGTCATTTTCTTCTGCTACG +GACAGCTGGTGTTCACAGTGAAGGAGGCGGCTGCCCAGCAGCAGGAGTCAGCCACCACCCAGAAGGCCGAGAAGGAAGTC +ACGCGCATGGTCATCATCATGGTCGTTGCGTTCCTAATCTGTTGGCTGCCCTACGCCAGCGTGGCATTCTACATCTTTAC +CCACCAGGGCTCTAACTTTGGCCCTGTCTTCATGACCATCCCGGCATTCTTCGCCAAGTCATCCTCCATCTACAACCCGG +TCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCCTCTGCTGTGGCAAGAACCCACTGGGTGAT +GACGAAGCATCCACCACTGCCTC >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 - +ATGAACGGGACCGAGGGCCCAAACTTCTACGTGCCTTTCTCCAACAAGACGGGCGTCGTACGCAGCCCCTTCGAGGCGCC +GCAGTACTACCTGGCTGAGCCATGGCAGTTCAGCATGCTGGCCGCCTACATGTTCCTGCTGATCATGCTTGGCTTCCCCA +TCAACTTCCTCACGCTGTACGTCACAGTCCAGCACAAGAAGCTGAGGACCCCCCTCAACTACATCCTGCTCAACCTGGCC +GTGGCAGATCTCTTCATGGTGTTCGGGGGCTTCACCACCACCCTGTATACCTCTCTGCACGGGTACTTCGTGTTCGGTCC +GACGGGCTGCAACCTCGAGGGCTTCTTTGCCACCTTAGGCGGTGAAATTGCACTGTGGTCCTTGGTGGTGCTAGCCATCG +AGCGGTACGTAGTGGTGTGCAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCACGCCATCATGGGCGTCGCATTCACC +TGGGTCATGGCTCTGGCCTGTGCGGCCCCCCCCCTCGTCGGCTGGTCTAGATACATCCCGGAGGGGATGCAGTGCTCGTG +CGGGATCGATTACTACACGCCCCACGAGGAGACCAACAATGAGTCGTTCGTCATCTACATGTTCGTTGTACACTTCATCA +TCCCCCTGATTGTCATATTCTTCTGCTACGGGCAGCTGGTCTTCACCGTCAAGGAGGCTGCAGCCCAGCAGCAGGAGTCG +GCCACCACTCAGAAGGCCGAGAAGGAGGTCACGCGTATGGTCATCATCATGGTCATCGCTTTCCTCATATGCTGGCTGCC +CTACGCAGGTGTGGCGTTCTACATCTTCACCCATCAGGGATCCGACTTTGGCCCCATCTTCATGACCATCCCGGCTTTCT +TTGCCAAGACGTCTGCCGTCTATAACCCCGTCATCTACATCATGATGAACAAGCAGTTCCGGAACTGCATGGTCACCACT +CTCTGCTGTGGCAAGAACCCCCTAGGTGACGACGAGGCCTCCACGACCGTGTCCAAGACAGAGACCAGCCAAGTGGCCCC +TGCCTAA >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 +CCGCTACTGACGAACCGCAACCATGAACGGCACTGAGGGACCTAACTTCTACATCCCCATGTCAAACGCCACTGGTGTAG +TGAGGAGTCCATTTGAATACCCGCAGTACTACCTTGCAGAACCATGGGCTTTCTCAGCTCTGTCTGCCTACATGTTCTTC +CTGATTATCGCCGGATTCCCCATCAACTTCCTCACCCTGTATGTCACCATCGAACATAAGAAACTGAGGACCCCACTGAA +CTACATTCTGCTGAACCTGGCCGTGGCCGACCTCTTCATGGTGTTTGGCGGATTCACCACCACGATGTACACCTCCATGC +ACGGCTACTTTGTCTTCGGCCCCACCGGCTGCAACATCGAAGGGTTCTTCGCCACCCTCGGCGGCGAGATTGCCCTCTGG +TGCCTCGTTGTCCTGGCCATTGAAAGGTGGATGGTCGTCTGCAAGCCAGTGACCAATTTCCGCTTCGGTGAGAGCCATGC +CATCATGGGTGTCATGGTGACCTGGACCATGGCATTGGCCTGTGCCCTCCCCCCTCTCTTCGGCTGGTCTCGGTACATTC +CGGAAGGTCTGCAGTGCTCGTGCGGGATCGACTACTATACCCGGGCGCCTGGGATCAACAATGAGTCCTTTGTGATCTAC +ATGTTTACCTGCCACTTCTCCATCCCACTCGCCGTCATCTCTTTCTGCTACGGCCGACTGGTGTGCACCGTCAAAGAGGC +CGCTGCCCAGCAACAGGAGTCCGAGACCACCCAGAGGGCTGAGCGGGAGGTCACCCGCATGGTCGTCATCATGGTCATCT +CCTTCCTGGTCTGCTGGGTGCCCTATGCCAGTGTGGCCTGGTACATCTTTACCCACCAGGGAAGCACTTTTGGGCCCATC +TTCATGACCATTCCATCCTTCTTTGCCAAGAGTTCAGCCCTCTACAACCCCATGATCTACATCTGCATGAACAAGCAGTT +CCGCCATTGCATGATCACCACCCTCTGCTGTGGGAAGAACCCCTTCGAGGAGGAGGATGGAGCGTCCGCCACTAGCTCTA +AAACTGAGGCTTCATCCGTGTCCTCCAGCTCTGTCTCCCCGGCATAAACCTTGTTTGACCGAACACCACGCATCAACACA +AAGACCAAGAATGCTGACTAAATGCTAACATTTCAGGGAAATCCAAAGACTTTTTACTATTTTTTTACACAACCATATAG +GTTGCAAACAGAGGTTTAGCCCTGTTTACAGGTTGTCATCAATGTGATGTCAGTATGTACAATATAGTCAACTTGATAGC +AAGTTGTTGGCTTATTTCAGATTGTATGGGCAATGTAATCAACCATATGTGAAATAAATTGCAA diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nhr Binary file test-data/rhodopsin_nucs.fasta.nhr has changed diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nin Binary file test-data/rhodopsin_nucs.fasta.nin has changed diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nnd Binary file test-data/rhodopsin_nucs.fasta.nnd has changed diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nni Binary file test-data/rhodopsin_nucs.fasta.nni has changed diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nog Binary file test-data/rhodopsin_nucs.fasta.nog has changed diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nsd --- a/test-data/rhodopsin_nucs.fasta.nsd Wed Mar 09 06:13:17 2016 -0500 +++ b/test-data/rhodopsin_nucs.fasta.nsd Mon Nov 07 11:29:43 2016 -0500 @@ -1,6 +1,13 @@ -gnl|bl_ord_id|00 -gnl|bl_ord_id|11 -gnl|bl_ord_id|22 -gnl|bl_ord_id|33 -gnl|bl_ord_id|44 -gnl|bl_ord_id|55 +ab0438175 +ab043817.15 +ab0624174 +ab062417.14 +bbu599211 +gq2903032 +gq290303.12 +gq2903123 +gq290312.13 +nm_0010092420 +nm_001009242.10 +u599211 +u59921.11 diff -r 4c47abb4c993 -r d8f2c1f560ec test-data/rhodopsin_nucs.fasta.nsi Binary file test-data/rhodopsin_nucs.fasta.nsi has changed diff -r 4c47abb4c993 -r d8f2c1f560ec tool-data/tool_data_table_conf.xml.sample --- a/tool-data/tool_data_table_conf.xml.sample Wed Mar 09 06:13:17 2016 -0500 +++ b/tool-data/tool_data_table_conf.xml.sample Mon Nov 07 11:29:43 2016 -0500 @@ -1,13 +1,13 @@ - +
value, name, path
- +
value, name, path
- +
value, name, path
diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/README.rst Mon Nov 07 11:29:43 2016 -0500 @@ -118,8 +118,9 @@ 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 +splitting if ``use_tasked_jobs = True`` is enabled in the ``config/galaxy.ini`` +configuration file (previously ``universe_wsgi.ini`` on older versions of +Galaxy). 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. @@ -229,7 +230,10 @@ (contribution from Bjoern Gruening and Daniel Blankenberg). v0.1.08 - Allow searching against multiple locally installed databases (contribution from Gildas Le Corguillé and Emma Prudent). - - Minor Python style changes (internal change only). + - Minor XML and Python style changes (internal change only). + - Set ``allow_duplicate_entries="False"`` in sample configuration file + ``tool_data_table_conf.xml``. + - Fix identifers with pipes in ``blastdbcmd`` wrapper (Devon Ryan). ======= ====================================================================== diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 @@ -16,8 +16,8 @@ -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('|','\|')" +##and make it comma separated. Quoted so don't escape pipes. +-entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',')" #end if ##When building a BLAST database, to ensure unique IDs makeblastdb will @@ -78,6 +78,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 @@ -74,7 +74,7 @@ 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/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 @@ -85,7 +85,7 @@ 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/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _DUST: http://www.ncbi.nlm.nih.gov/pubmed/16796549 **References** diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Mon Nov 07 11:29:43 2016 -0500 @@ -133,7 +133,7 @@ - + @@ -156,7 +156,7 @@ - + @@ -296,7 +296,7 @@ - + diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Nov 07 11:29:43 2016 -0500 @@ -190,7 +190,7 @@ **Documentation** -http://www.ncbi.nlm.nih.gov/books/NBK1763/ +https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Mon Nov 07 11:29:43 2016 -0500 @@ -113,7 +113,7 @@ 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/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 @@ -77,14 +77,14 @@ *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/ +counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ *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/ +on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/ *Pfam* - PSSMs from Pfam-A seed alignment database, see -http://pfam.sanger.ac.uk/ +http://xfam.org/ *Smart* - PSSMs from SMART domain alignment database, see http://smart.embl-heidelberg.de/ diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 @@ -77,14 +77,14 @@ *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/ +counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/ *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/ +on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/ *Pfam* - PSSMs from Pfam-A seed alignment database, see -http://pfam.sanger.ac.uk/ +http://xfam.org/ *Smart* - PSSMs from SMART domain alignment database, see http://smart.embl-heidelberg.de/ diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Mon Nov 07 11:29:43 2016 -0500 @@ -87,7 +87,7 @@ 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/ +.. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ .. _SEG: http://www.ncbi.nlm.nih.gov/pubmed/8743706 **References** diff -r 4c47abb4c993 -r d8f2c1f560ec tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Wed Mar 09 06:13:17 2016 -0500 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Mon Nov 07 11:29:43 2016 -0500 @@ -1,6 +1,6 @@ - +