[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8e7c00f4352f/ changeset: r5437:8e7c00f4352f user: peterjc date: 2011-04-19 17:08:18 summary: Fix BLAST+ HTML output affected #: 5 files (5 bytes) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Apr 19 14:45:55 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Apr 19 16:08:18 2011 +0100 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.9"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.10"><description>Search nucleotide database with nucleotide query sequence(s)</description><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. @@ -17,7 +17,7 @@ #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: - -outfmt "$out_format" + -outfmt $out_format #end if -num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Apr 19 14:45:55 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Apr 19 16:08:18 2011 +0100 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.9"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.10"><description>Search protein database with protein query sequence(s)</description><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. @@ -17,7 +17,7 @@ #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: - -outfmt "$out_format" + -outfmt $out_format #end if -num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Apr 19 14:45:55 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Apr 19 16:08:18 2011 +0100 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.9"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.10"><description>Search protein database with translated nucleotide query sequence(s)</description><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. @@ -16,7 +16,7 @@ #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: - -outfmt "$out_format" + -outfmt $out_format #end if -num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Apr 19 14:45:55 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Apr 19 16:08:18 2011 +0100 @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.9"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.10"><description>Search translated nucleotide database with protein query sequence(s)</description><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. @@ -16,7 +16,7 @@ #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: - -outfmt "$out_format" + -outfmt $out_format #end if -num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Apr 19 14:45:55 2011 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Apr 19 16:08:18 2011 +0100 @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.9"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.10"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. @@ -16,7 +16,7 @@ #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: - -outfmt "$out_format" + -outfmt $out_format #end if -num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": http://bitbucket.org/galaxy/galaxy-central/changeset/531f2d20469a/ changeset: r5438:531f2d20469a user: peterjc date: 2011-04-19 17:20:52 summary: BLAST+ HTML output test affected #: 2 files (20.1 KB) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Tue Apr 19 16:20:52 2011 +0100 @@ -0,0 +1,787 @@ +<HTML> +<TITLE>BLAST Search Results</TITLE> +<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> +<PRE> + +<b>TBLASTN 2.2.25+</b> + + +<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 +OS=Homo sapiens GN=ERP44 PE=1 SV=1 + +Length=406 + +<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + +Length=1047 + + +***** No hits found ***** + + + +Lambda K H + 0.347 0.182 0.684 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 127710 + + +<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 +OS=Homo sapiens GN=ERP44 PE=1 SV=1 + +Length=406 + +<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete +cds + +Length=1574 + + +***** No hits found ***** + + + +Lambda K H + 0.347 0.182 0.684 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 127710 + + +<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 +OS=Homo sapiens GN=ERP44 PE=1 SV=1 + +Length=406 + +<b>Subject=</b> 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 + 0.347 0.182 0.684 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 127710 + + +<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 +OS=Homo sapiens GN=ERP44 PE=1 SV=1 + +Length=406 + +<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin +(RHO) mRNA, partial cds + +Length=983 + + +***** No hits found ***** + + + +Lambda K H + 0.347 0.182 0.684 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 127710 + + +<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 +OS=Homo sapiens GN=ERP44 PE=1 SV=1 + +Length=406 + +<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for +rhodopsin, complete cds + +Length=1047 + + +***** No hits found ***** + + + +Lambda K H + 0.347 0.182 0.684 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 127710 + + +<b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 +OS=Homo sapiens GN=ERP44 PE=1 SV=1 + +Length=406 + +<b>Subject=</b> 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 + 0.347 0.182 0.684 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 127710 + + +<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens +GN=BMP2K PE=1 SV=2 + +Length=1161 + +<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + +Length=1047 + + +***** No hits found ***** + + + +Lambda K H + 0.334 0.170 0.615 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 370988 + + +<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens +GN=BMP2K PE=1 SV=2 + +Length=1161 + +<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete +cds + +Length=1574 + + +***** No hits found ***** + + + +Lambda K H + 0.334 0.170 0.615 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 370988 + + +<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens +GN=BMP2K PE=1 SV=2 + +Length=1161 + +<b>Subject=</b> 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 + 0.334 0.170 0.615 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 370988 + + +<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens +GN=BMP2K PE=1 SV=2 + +Length=1161 + +<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin +(RHO) mRNA, partial cds + +Length=983 + + +***** No hits found ***** + + + +Lambda K H + 0.334 0.170 0.615 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 370988 + + +<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens +GN=BMP2K PE=1 SV=2 + +Length=1161 + +<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for +rhodopsin, complete cds + +Length=1047 + + +***** No hits found ***** + + + +Lambda K H + 0.334 0.170 0.615 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 370988 + + +<b>Query=</b> sp|Q9NSY1|BMP2K_HUMAN BMP-2-inducible protein kinase OS=Homo sapiens +GN=BMP2K PE=1 SV=2 + +Length=1161 + +<b>Subject=</b> 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 + 0.334 0.170 0.615 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 370988 + + +<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 +SV=4 + +Length=1382 + +<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + +Length=1047 + + +***** No hits found ***** + + + +Lambda K H + 0.346 0.180 0.700 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 441350 + + +<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 +SV=4 + +Length=1382 + +<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete +cds + +Length=1574 + + +***** No hits found ***** + + + +Lambda K H + 0.346 0.180 0.700 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 441350 + + +<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 +SV=4 + +Length=1382 + +<b>Subject=</b> 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 + 0.346 0.180 0.700 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 441350 + + +<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 +SV=4 + +Length=1382 + +<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin +(RHO) mRNA, partial cds + +Length=983 + + +***** No hits found ***** + + + +Lambda K H + 0.346 0.180 0.700 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 441350 + + +<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 +SV=4 + +Length=1382 + +<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for +rhodopsin, complete cds + +Length=1047 + + +***** No hits found ***** + + + +Lambda K H + 0.346 0.180 0.700 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 441350 + + +<b>Query=</b> sp|P06213|INSR_HUMAN Insulin receptor OS=Homo sapiens GN=INSR PE=1 +SV=4 + +Length=1382 + +<b>Subject=</b> 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 + 0.346 0.180 0.700 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 441350 + + +<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + +Length=348 + +<b>Subject=</b> gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA + +Length=1047 + +<script src="blastResult.js"></script> + 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 + 0.351 0.182 0.707 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 109230 + + +<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + +Length=348 + +<b>Subject=</b> gi|2734705|gb|U59921.1|BBU59921 Bufo bufo rhodopsin mRNA, complete +cds + +Length=1574 + +<script src="blastResult.js"></script> + 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 + 0.351 0.182 0.707 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 109230 + + +<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + +Length=348 + +<b>Subject=</b> gi|283855845|gb|GQ290303.1| Cynopterus brachyotis voucher 20020434 +rhodopsin (RHO) gene, exons 1 through 5 and partial cds + +Length=4301 + +<script src="blastResult.js"></script> + Score = 151 bits (342), Expect(2) = 1e-72, Method: Compositional matrix adjust. + Identities = 69/74 (94%), 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 = 1e-64, Method: Compositional matrix adjust. + Identities = 107/111 (97%), Positives = 109/111 (99%), 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 (94%), 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 = 6e-13, Method: Compositional matrix adjust. + Identities = 23/26 (89%), Positives = 24/26 (93%), Gaps = 0/26 (0%) + Frame = +1 + +Query 312 QFRNCMLTTICCGKNPLGDDEASATV 337 + QFRNCMLTT+CCGKNPLGDDEAS T +Sbjct 4222 QFRNCMLTTLCCGKNPLGDDEASTTA 4299 + + + +Lambda K H + 0.351 0.182 0.707 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 109230 + + +<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + +Length=348 + +<b>Subject=</b> gi|283855822|gb|GQ290312.1| Myotis ricketti voucher GQX10 rhodopsin +(RHO) mRNA, partial cds + +Length=983 + +<script src="blastResult.js"></script> + Score = 658 bits (1517), Expect = 0.0, Method: Compositional matrix adjust. + Identities = 310/326 (96%), 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 + 0.351 0.182 0.707 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 109230 + + +<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + +Length=348 + +<b>Subject=</b> gi|18148870|dbj|AB062417.1| Synthetic construct Bos taurus gene for +rhodopsin, complete cds + +Length=1047 + +<script src="blastResult.js"></script> + Score = 711 bits (1640), Expect = 0.0, Method: Compositional matrix adjust. + Identities = 325/348 (94%), 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 + 0.351 0.182 0.707 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 109230 + + +<b>Query=</b> sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1 + +Length=348 + +<b>Subject=</b> gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh +water form rod opsin, complete cds + +Length=1344 + +<script src="blastResult.js"></script> + Score = 626 bits (1444), Expect = 0.0, Method: Compositional matrix adjust. + Identities = 281/342 (83%), 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 + 0.351 0.182 0.707 + +Gapped +Lambda K H + 0.299 0.0710 0.270 + +Effective search space used: 109230 + + + + +Matrix: BLOSUM80 +Gap Penalties: Existence: 10, Extension: 1 +Neighboring words threshold: 14 +Window for multiple hits: 25 +</PRE> +</BODY> +</HTML> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Apr 19 16:08:18 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Apr 19 16:20:52 2011 +0100 @@ -188,6 +188,21 @@ <param name="parse_deflines" value="true" /><output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /></test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="0 -html" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <param name="matrix" value="BLOSUM80" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="false" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" /> + </test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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