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changeset 12:d8f2c1f560ec draft

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Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
author peterjc
date Mon, 07 Nov 2016 11:29:43 -0500
parents 4c47abb4c993
children 4dcc9429d6d2
files test-data/rhodopsin_bufo.fasta test-data/rhodopsin_nucs.dbinfo.txt test-data/rhodopsin_nucs.fasta test-data/rhodopsin_nucs.fasta.nhr test-data/rhodopsin_nucs.fasta.nin test-data/rhodopsin_nucs.fasta.nnd test-data/rhodopsin_nucs.fasta.nni test-data/rhodopsin_nucs.fasta.nog test-data/rhodopsin_nucs.fasta.nsd test-data/rhodopsin_nucs.fasta.nsi tool-data/tool_data_table_conf.xml.sample tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_makeprofiledb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml tools/ncbi_blast_plus/tool_dependencies.xml
diffstat 22 files changed, 218 insertions(+), 185 deletions(-) [+]
line wrap: on
line diff
--- /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
--- 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
--- 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
Binary file test-data/rhodopsin_nucs.fasta.nhr has changed
Binary file test-data/rhodopsin_nucs.fasta.nin has changed
Binary file test-data/rhodopsin_nucs.fasta.nnd has changed
Binary file test-data/rhodopsin_nucs.fasta.nni has changed
Binary file test-data/rhodopsin_nucs.fasta.nog has changed
--- 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
Binary file test-data/rhodopsin_nucs.fasta.nsi has changed
--- 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 @@
 <tables>
-    <table name="blastdb" comment_char="#">
+    <table name="blastdb" comment_char="#" allow_duplicate_entries="False">
         <columns>value, name, path</columns>
         <file path="tool-data/blastdb.loc" />
     </table>
-    <table name="blastdb_p" comment_char="#">
+    <table name="blastdb_p" comment_char="#" allow_duplicate_entries="False">
         <columns>value, name, path</columns>
         <file path="tool-data/blastdb_p.loc" />
     </table>
-    <table name="blastdb_d" comment_char="#">
+    <table name="blastdb_d" comment_char="#" allow_duplicate_entries="False">
         <columns>value, name, path</columns>
         <file path="tool-data/blastdb_d.loc" />
     </table>
--- 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).
 ======= ======================================================================
 
 
--- 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 @@
             <param name="outfmt" value="original" />
             <output name="seq" file="four_human_proteins.fasta" ftype="fasta" />
         </test>
+        <test>
+            <param name="db_opts|db_type" value="nucl" />
+            <param name="db_opts|database" value="rhodopsin_nucs" />
+            <param name="id_opts|id_type" value="prompt" />
+            <param name="id_opts|entries" value="all" />
+            <param name="outfmt" value="original" />
+            <output name="seq" file="rhodopsin_nucs.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="db_opts|db_type" value="nucl" />
+            <param name="db_opts|database" value="rhodopsin_nucs" />
+            <param name="id_opts|id_type" value="prompt" />
+            <param name="id_opts|entries" value="U59921.1" />
+            <param name="outfmt" value="original" />
+            <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="db_opts|db_type" value="nucl" />
+            <param name="db_opts|database" value="rhodopsin_nucs" />
+            <param name="id_opts|id_type" value="prompt" />
+            <param name="id_opts|entries" value="gi|2734705|gb|U59921.1|BBU59921" />
+            <param name="outfmt" value="original" />
+            <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
+        </test>
     </tests>
     <help>
     
--- 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**
 
--- 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**
--- 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 @@
     <xml name="input_query_gencode">
         <param name="query_gencode" type="select" label="Query genetic code">
             <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
-            <option value="1" select="True">1. Standard</option>
+            <option value="1" selected="True">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
             <option value="3">3. Yeast Mitochondrial</option>
             <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
@@ -156,7 +156,7 @@
     <xml name="input_db_gencode">
         <param name="db_gencode" type="select" label="Database/subject genetic code">
             <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
-            <option value="1" select="True">1. Standard</option>
+            <option value="1" selected="True">1. Standard</option>
             <option value="2">2. Vertebrate Mitochondrial</option>
             <option value="3">3. Yeast Mitochondrial</option>
             <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
@@ -296,7 +296,7 @@
         </param>
     </xml>
     <xml name="input_qcov_hsp_perc">
-        <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qhspcov"/>
+        <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qcovhsp"/>
     </xml>
     <xml name="advanced_options">
         <conditional name="adv_opts">
--- 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**
 
--- 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**
--- 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/
--- 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/
--- 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**
--- 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 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="blast+" version="2.2.31">
-        <repository changeset_revision="4df9cdbc6e61" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="6e4a0aaa3357" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>