Mercurial > repos > devteam > ncbi_blast_plus
changeset 10:70e7dcbf6573 draft
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_rhodopsin_vs_three_human.tabular Mon Sep 23 06:14:13 2013 -0400 @@ -0,0 +1,7 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.10 1050 77 6 1 1047 88 1134 0.0 1474 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 333 28 0 1 333 118 450 9e-133 460 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.36 243 19 2 3127 3368 782 1023 7e-94 331 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 94.22 173 10 0 1410 1582 448 620 8e-74 265 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.98 171 10 2 2854 3023 615 784 8e-69 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.58 962 75 6 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.55 1052 121 10 1 1047 88 1134 0.0 1208
--- a/test-data/blastp_four_human_vs_rhodopsin_converted.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted.tabular Mon Sep 23 06:14:13 2013 -0400 @@ -3,4 +3,4 @@ sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 3e-176 599 +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599
--- a/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin_converted_ext.tabular Mon Sep 23 06:14:13 2013 -0400 @@ -3,4 +3,4 @@ sp|P08100|OPSD_HUMAN gi|283855846|gb|ADB45242.1| 94.82 328 17 0 11 338 1 328 0.0 653 gi|283855846|gb|ADB45242.1| 1684 311 321 0 97.87 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 sp|P08100|OPSD_HUMAN gi|283855823|gb|ADB45229.1| 94.82 328 17 0 11 338 1 328 0.0 631 gi|283855823|gb|ADB45229.1| 1627 311 323 0 98.48 1 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVS VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTAS 348 328 sp|P08100|OPSD_HUMAN gi|223523|prf||0811197A 93.10 348 23 1 1 348 1 347 0.0 673 gi|223523|prf||0811197A 1736 324 336 1 96.55 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 347 -sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 3e-176 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354 +sp|P08100|OPSD_HUMAN gi|12583665|dbj|BAB21486.1| 82.16 342 60 1 1 341 1 342 0.0 599 gi|12583665|dbj|BAB21486.1| 1544 281 314 1 91.81 1 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 354
--- a/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Mon Sep 23 06:14:13 2013 -0400 @@ -1,10 +1,10 @@ gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 1e-168 575 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-62 224 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-34 129 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 2e-31 120 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-30 118 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 6e-12 56.2 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 2e-180 613 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 6e-164 559 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559
--- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Thu Apr 25 09:38:37 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Mon Sep 23 06:14:13 2013 -0400 @@ -1,10 +1,10 @@ gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 662 sp|P08100|OPSD_HUMAN 1707 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 1e-168 575 sp|P08100|OPSD_HUMAN 1481 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-62 224 sp|P08100|OPSD_HUMAN 570 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-34 129 sp|P08100|OPSD_HUMAN 324 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 2e-31 120 sp|P08100|OPSD_HUMAN 302 54 56 0 100.00 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-30 118 sp|P08100|OPSD_HUMAN 295 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 -gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 6e-12 56.2 sp|P08100|OPSD_HUMAN 134 23 24 0 96.00 1 0 QFRNCMLTTLCCGKNPLGDDEASTT QFRNCMLTTICCGKNPLGDDEASAT 4301 348 -gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 2e-180 613 sp|P08100|OPSD_HUMAN 1582 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 575 sp|P08100|OPSD_HUMAN 1481 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 2e-68 224 sp|P08100|OPSD_HUMAN 570 107 109 0 98.20 1 0 VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 5e-36 129 sp|P08100|OPSD_HUMAN 324 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.43 56 2 0 2855 3022 177 232 3e-33 120 sp|P08100|OPSD_HUMAN 302 54 56 0 100.00 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 2e-32 118 sp|P08100|OPSD_HUMAN 295 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.00 25 2 0 4222 4296 312 336 2e-12 56.2 sp|P08100|OPSD_HUMAN 134 23 24 0 96.00 1 0 QFRNCMLTTLCCGKNPLGDDEASTT QFRNCMLTTICCGKNPLGDDEASAT 4301 348 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 613 sp|P08100|OPSD_HUMAN 1582 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 641 sp|P08100|OPSD_HUMAN 1654 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 -gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 6e-164 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.93 332 60 0 23 1018 1 332 0.0 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tblastx_rhodopsin_vs_three_human.tabular Mon Sep 23 06:14:13 2013 -0400 @@ -0,0 +1,117 @@ +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 97.39 230 6 0 1 690 88 777 0.0 559 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 94.12 102 6 0 742 1047 829 1134 0.0 236 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 91.22 148 13 0 1046 603 1133 690 0.0 308 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 94.32 88 5 0 566 303 653 390 0.0 207 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 96.34 82 3 0 248 3 335 90 0.0 182 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 83.33 204 34 0 18 629 105 716 4e-158 404 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 75.28 89 22 0 780 1046 867 1133 4e-158 161 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 81.28 203 38 0 609 1 696 88 5e-153 360 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 80.60 67 13 0 916 716 1003 803 5e-153 135 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 70.27 37 11 0 1047 937 1134 1024 5e-153 64.2 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 100.00 7 0 0 646 626 733 713 5e-153 24.0 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 89.23 65 7 0 460 266 547 353 4e-105 167 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 89.58 48 5 0 184 41 271 128 4e-105 104 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 77.78 45 10 0 882 748 969 835 4e-105 93.9 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 67.86 28 9 0 1045 962 1132 1049 4e-105 51.9 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 59.09 22 9 0 586 521 673 608 4e-105 33.1 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 81.40 86 16 0 296 553 383 640 2e-87 185 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 84.38 32 5 0 11 106 98 193 2e-87 74.8 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 71.43 35 10 0 941 1045 1028 1132 2e-87 61.6 +gi|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 94.44 18 1 0 794 847 881 934 2e-87 50.1 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 83.61 238 39 0 18 731 64 777 0.0 507 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 82.35 85 15 0 783 1037 829 1083 0.0 188 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 70.96 303 88 0 925 17 971 63 2e-130 435 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 72.22 18 5 0 1027 974 1073 1020 2e-130 35.0 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 55.32 188 84 0 605 42 651 88 7e-89 245 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 61.11 72 28 0 1037 822 1083 868 7e-89 91.3 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 49.02 204 104 0 29 640 75 686 4e-78 197 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 66.04 53 18 0 860 1018 906 1064 4e-78 85.8 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 44.44 27 15 0 689 769 735 815 4e-78 32.2 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 47.47 198 104 0 633 40 679 86 4e-65 177 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 68.09 47 15 0 1017 877 1063 923 4e-65 80.3 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 57.89 114 48 0 265 606 311 652 3e-46 137 +gi|2734705|gb|U59921.1|BBU59921 ENA|BC112106|BC112106.1 46.30 54 29 0 19 180 65 226 3e-46 52.4 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 96.40 111 4 0 1 333 118 450 0.0 264 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.31 65 5 0 3174 3368 829 1023 0.0 151 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 96.43 56 2 0 2855 3022 616 783 0.0 141 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 93.22 59 4 0 1404 1580 442 618 0.0 138 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.00 25 2 0 4222 4296 1021 1095 0.0 64.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 88.89 9 1 0 3128 3154 783 809 0.0 22.6 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 78.38 111 24 0 333 1 450 118 7e-171 212 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 88.75 80 9 0 3367 3128 1022 783 7e-171 161 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 93.33 60 4 0 1582 1403 620 441 7e-171 136 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.07 56 5 0 3021 2854 782 615 7e-171 119 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 84.62 26 4 0 4301 4224 1100 1023 7e-171 52.8 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 95.83 72 3 0 218 3 335 120 8e-142 152 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 77.78 63 14 0 3368 3180 1023 835 8e-142 125 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 85.11 47 7 0 1544 1404 582 442 8e-142 108 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.36 56 11 0 3022 2855 783 616 8e-142 101 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 75.86 29 7 0 325 239 442 356 8e-142 58.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 86.36 22 3 0 4287 4222 1086 1021 8e-142 48.7 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 90.91 11 1 0 3159 3127 814 782 8e-142 31.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 81.03 58 11 0 2854 3027 615 788 2e-122 128 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 83.33 60 10 0 1403 1582 441 620 2e-122 125 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.60 67 13 0 3 203 120 320 2e-122 119 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.30 23 2 0 4220 4288 1019 1087 2e-122 53.8 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 78.26 23 5 0 266 334 383 451 2e-122 48.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.00 20 4 0 3308 3367 963 1022 2e-122 46.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 83.33 18 3 0 3226 3279 881 934 2e-122 40.5 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 80.39 51 10 0 154 2 271 119 1e-92 97.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 73.68 57 15 0 3366 3196 1021 851 1e-92 95.9 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 81.82 44 8 0 1521 1390 559 428 1e-92 95.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 95.00 20 1 0 332 273 449 390 1e-92 52.4 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 86.36 22 3 0 4288 4223 1087 1022 1e-92 48.3 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 61.54 26 10 0 2912 2835 673 596 1e-92 37.7 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 69.57 23 7 0 3023 2955 784 716 1e-92 33.1 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 76.67 30 7 0 2 91 119 208 6e-43 68.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.11 45 4 0 1411 1545 449 583 6e-43 68.0 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 77.27 22 5 0 267 332 384 449 6e-43 45.1 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 86.36 22 3 0 4224 4289 1023 1088 6e-43 44.1 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 83.33 12 2 0 2856 2891 617 652 6e-43 25.4 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 95.91 220 9 0 1 660 118 777 0.0 526 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 92.13 89 7 0 712 978 829 1095 0.0 212 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.01 178 16 0 536 3 653 120 1e-178 353 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 88.32 137 16 0 983 573 1100 690 1e-178 277 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 77.43 319 72 0 3 959 120 1076 4e-174 593 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 79.07 129 27 0 558 172 675 289 2e-133 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 76.83 82 19 0 963 718 1080 835 2e-133 159 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 84.09 44 7 0 133 2 250 119 2e-133 97.3 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 73.08 78 21 0 433 200 550 317 6e-102 145 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 70.15 67 20 0 799 599 916 716 6e-102 106 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 80.49 41 8 0 123 1 240 118 6e-102 84.5 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 77.78 27 6 0 553 473 670 590 6e-102 51.9 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 71.43 14 4 0 889 848 1006 965 6e-102 32.7 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 81.82 11 2 0 958 926 1075 1043 6e-102 28.6 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 84.85 33 5 0 239 337 356 454 4e-48 72.5 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 86.67 30 4 0 2 91 119 208 4e-48 71.2 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 81.40 43 8 0 404 532 521 649 4e-48 47.3 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 88.89 18 2 0 764 817 881 934 4e-48 44.6 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 87.50 8 1 0 935 958 1052 1075 4e-48 21.7 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 93.91 230 14 0 1 690 88 777 0.0 538 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 91.18 102 9 0 742 1047 829 1134 0.0 233 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 88.83 188 21 0 566 3 653 90 0.0 394 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 84.06 138 22 0 1046 633 1133 720 0.0 260 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 67.11 228 75 0 684 1 771 88 7e-132 333 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 67.27 110 36 0 1045 716 1132 803 7e-132 141 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 70.20 151 45 0 3 455 90 542 1e-128 236 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 64.04 89 32 0 780 1046 867 1133 1e-128 136 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 66.22 74 25 0 510 731 597 818 1e-128 111 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 66.04 106 36 0 242 559 329 646 2e-58 161 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 85.71 21 3 0 92 154 179 241 2e-58 53.8 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 73.68 19 5 0 791 847 878 934 2e-58 39.1 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 61.29 62 24 0 424 239 511 326 4e-55 81.3 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 74.36 39 10 0 133 17 220 104 4e-55 69.8 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 65.71 35 12 0 882 778 969 865 4e-55 56.3 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 58.14 43 18 0 649 521 736 608 4e-55 50.6 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 66.67 12 4 0 972 937 1059 1024 4e-55 23.9 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 82.13 235 42 0 11 715 76 780 0.0 498 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 78.31 83 18 0 770 1018 835 1083 0.0 177 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 72.29 332 92 0 1017 22 1082 87 1e-150 516 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 48.30 147 76 0 712 272 777 337 2e-98 169 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 54.17 72 33 0 1030 815 1095 880 2e-98 103 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 47.83 69 36 0 220 14 285 79 2e-98 83.5 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 72.00 25 7 0 782 708 847 773 2e-98 45.1 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 56.00 75 33 0 532 756 597 821 5e-65 87.7 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 39.42 104 63 0 19 330 84 395 5e-65 86.8 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 56.90 58 25 0 829 1002 894 1067 5e-65 81.3 +gi|12583664|dbj|AB043817.1| ENA|BC112106|BC112106.1 50.00 30 15 0 388 477 453 542 5e-65 33.6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/three_human_mRNA.fasta Mon Sep 23 06:14:13 2013 -0400 @@ -0,0 +1,183 @@ +>ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds. +GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAG +CCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCAC +GGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTC +CCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGA +TACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGC +TGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCAT +TAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCA +CTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAA +TGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTA +CATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCAC +TCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTA +TAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATT +TGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGG +GCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAA +TTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGA +ATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAG +TTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAA +CTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCC +AGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTT +CAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAA +ACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGC +CCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATA +TAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAG +CCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTC +TATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCC +CCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTA +GGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTT +ATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTA +GGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATT +CTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTT +GGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATA +TTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATA +CTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACA +AGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATG +GATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGG +AACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAAT +TTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCT +TGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTT +TTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGG +CCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAA +CCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGT +TCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATAC +TTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACAT +GTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATT +AATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGT +TATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGT +GATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTT +TCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAA +GTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAA +TTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAA +TATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTT +AGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGT +TCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATT +ACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCT +GGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTA +GAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGT +GACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATT +TTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTT +TTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTT +AGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTG +AGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGC +TGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTT +CACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAA +GACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACAT +TATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCT +GAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCT +TTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGG +GCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAA +CAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCA +CGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTA +GAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGA +GGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCT +GCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATG +GAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCA +ATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCA +AAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAA +ATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAA +GGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGAT +AAAGTAGTGTAATGGATTGACAATCAGGAAGAACAGAATAACTCAGTTTTTTTTTCTCCT +ACAAGGAGATATGGCTGGACCAAAATAAAATGACATGAAATTGCAAAAATGAAAAT +>ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds. +GGGGGGCTGCGCGGCCGGGTCGGTGCGCACACGAGAAGGACGCGCGGCCCCCAGCGCTCT +TGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGA +CCCCGCGCTCCCGCAGCCATGGGCACCGGGGGCCGGCGGGGGGCGGCGGCCGCGCCGCTG +CTGGTGGCGGTGGCCGCGCTGCTACTGGGCGCCGCGGGCCACCTGTACCCCGGAGAGGTG +TGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCT +GTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGA +GACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTAT +GGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTG +TTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTAC +AACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTAC +TTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTG +AACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACC +AACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCAC +TGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGT +TGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCC +TGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCAC +TTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAG +AACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAG +TGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCC +TGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCC +CAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGC +AACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTAT +CTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTG +ATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAAC +CTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTC +TTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGA +ACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCC +TGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTG +AGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTAC +AAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAAC +AGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAAC +CACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAG +ACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTAT +GTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCA +TCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCAC +TACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGC +CTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCT +CAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAG +ACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGAT +TACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGAC +CCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTG +CCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAG +CACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACAC +TTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGC +AGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTT +GGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCG +AAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAG +GAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGT +GGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGC +TCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATT +GCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGT +ATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCT +TCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGAC +GAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTC +GGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTG +GCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAG +GCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCC +AAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTAC +CTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAA +GAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAG +TTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAA +ATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGC +AAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACC +ACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAA +CAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTAT +CTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAA +TTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTG +CACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGT +GAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCAC +TGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGC +TACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTG +ACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTT +CCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCT +ACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGAC +TCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAA +GGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGT +TTTTTCGTTCCCCCCACCCGCCCCCAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATT +CTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGGTGTCTGAGCTTCAGTATAAAAGACAA +AACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA +>ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds. +CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGC +CACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTG +CCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTG +GCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGC +TTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCT +CTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTC +ACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAAT +TTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTG +GCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAAC +CATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCA +CTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTAC +TACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCAC +TTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAG +GAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACC +CGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTG +GCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCA +GCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAG +CAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGAT +GAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTG +CCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACA +GCCATCCCACCAG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/README.rst Mon Sep 23 06:14:13 2013 -0400 @@ -0,0 +1,168 @@ +Galaxy wrappers for NCBI BLAST+ suite +===================================== + +These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), +and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). + +Note that these wrappers (and the associated datatypes) were originally +distributed as part of the main Galaxy repository, but as of August 2012 +moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). +My thanks to Dannon Baker from the Galaxy development team for his assistance +with this. + +These wrappers are available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + + +Automated Installation +====================== + +Galaxy should be able to automatically install the dependencies, i.e. the +'blast_datatypes' repository which defines the BLAST XML file format +('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and +'blastdbn'). + +You must tell Galaxy about any system level BLAST databases using configuration +files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein +databases like NR), and blastdb_d.loc (protein domain databases like CDD or +SMART) which are located in the tool-data/ folder. Sample files are included +which explain the tab-based format to use. + +You can download the NCBI provided databases as tar-balls from here: + +* ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) +* ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) + + +Manual Installation +=================== + +For those not using Galaxy's automated installation from the Tool Shed, put +the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML +files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample +in order to run the unit tests). For example, use:: + + <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> + <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> + <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> + <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" /> + <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> + </section> + +You will also need to install 'blast_datatypes' from the Tool Shed. This +defines the BLAST XML file format ('blastxml') and protein and nucleotide +BLAST databases composite file formats ('blastdbp' and 'blastdbn'). + +As described above for an automated installation, you must also tell Galaxy +about any system level BLAST databases using the tool-data/blastdb*.loc files. + +You must install the NCBI BLAST+ standalone tools somewhere on the system +path. Currently the unit tests are written using "BLAST 2.2.26+". + +Run the functional tests (adjusting the section identifier to match your +tool_conf.xml.sample file):: + + ./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.11 - Final revision as part of the Galaxy main repository, and the + first release via the Tool Shed +v0.0.12 - Implements genetic code option for translation searches. + - Changes <parallelism> to 1000 sequences at a time (to cope with + very large sets of queries where BLAST+ can become memory hungry) + - Include warning that BLAST+ with subject FASTA gives pairwise + e-values +v0.0.13 - Use the new error handling options in Galaxy (the previously + bundled hide_stderr.py script is no longer needed). +v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases + in the history (using work from Edward Kirton), requires v0.0.14 + of the 'blast_datatypes' repository from the Tool Shed. +v0.0.15 - Stronger warning in help text against searching against subject + FASTA files (better looking e-values than you might be expecting). +v0.0.16 - Added repository_dependencies.xml for automates installation of the + 'blast_datatypes' repository from the Tool Shed. +v0.0.17 - The BLAST+ search tools now default to extended tabular output + (all too often our users where having to re-run searches just to + get one of the missing columns like query or subject length) +v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, + BLAST+ handling of some mult-file arguments is problematic). +v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc + for the domain databases they use (e.g. CDD, PFAM or SMART). + - Correct case of exception regular expression (for error handling + fall-back in case the return code is not set properly). + - Clearer naming of output files. +v0.0.20 - Added unit tests for BLASTN and TBLASTX. + - Added percentage identity option to BLASTN. + - Fallback on ElementTree if cElementTree missing in XML to tabular. + - Link to Tool Shed added to help text and this documentation. + - Tweak dependency on blast_datatypes to also work on Test Tool Shed. + - Dependency on new package_blast_plus_2_2_26 in Tool Shed. + - Adopted standard MIT License. + - Development moved to GitHub, https://github.com/peterjc/galaxy_blast + - Updated citation information (Cock et al. 2013). +======= ====================================================================== + + +Bug Reports +=========== + +You can file an issue here https://github.com/peterjc/galaxy_blast/issues or ask +us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev + + +Developers +========== + +This script and related tools were originally developed on the 'tools' branch +of the following Mercurial repository: +https://bitbucket.org/peterjc/galaxy-central/ + +As of July 2013, development is continuing on a dedicated GitHub repository: +https://github.com/peterjc/galaxy_blast + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use +the following command from the GitHub repository root folder:: + + $ ./ncbi_blast_plus/make_ncbi_blast_plus.sh + +This simplifies ensuring a consistent set of files is bundled each time, +including all the relevant test files. + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Mon Sep 23 06:14:13 2013 -0400 @@ -1,5 +1,5 @@ #!/usr/bin/env python -"""Convert a BLAST XML file to 12 column tabular output +"""Convert a BLAST XML file to tabular output. Takes three command line options, input BLAST XML filename, output tabular BLAST filename, output format (std for standard 12 columns, or ext for the @@ -62,8 +62,15 @@ import sys import re +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.12" + sys.exit(0) + if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as ElementTree + try: + from xml.etree import cElementTree as ElementTree + except ImportError: + from xml.etree import ElementTree as ElementTree else: from galaxy import eggs import pkg_resources; pkg_resources.require( "elementtree" )
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,5 +1,6 @@ -<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.10"> +<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.11"> <description>Convert BLAST XML output to tabular</description> + <version_command interpreter="python">blastxml_to_tabular.py --version</version_command> <command interpreter="python"> blastxml_to_tabular.py $blastxml_file $tabular_file $out_format </command> @@ -128,5 +129,17 @@ low complexity (columns 21 and 22), and thus also calculated figures like the percentage identity (column 3). +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu Apr 25 09:38:37 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,144 +0,0 @@ -Galaxy wrappers for NCBI BLAST+ suite -===================================== - -These wrappers are copyright 2010-2013 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), -and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). - -Note that these wrappers (and the associated datatypes) were originally -distributed as part of the main Galaxy repository, but as of August 2012 -moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes'). -My thanks to Dannon Baker from the Galaxy development team for his assistance -with this. - - -Automated Installation -====================== - -Galaxy should be able to automatically install the dependencies, i.e. the -'blast_datatypes' repository which defines the BLAST XML file format -('blastxml') and protein and nucleotide BLAST databases ('blastdbp' and -'blastdbn'). - -You must tell Galaxy about any system level BLAST databases using configuration -files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein -databases like NR), and blastdb_d.loc (protein domain databases like CDD or -SMART) which are located in the tool-data/ folder. Sample files are included -which explain the tab-based format to use. - -You can download the NCBI provided databases as tar-balls from here: -ftp://ftp.ncbi.nlm.nih.gov/blast/db/ (nucleotide and protein databases like NR) -ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/little_endian/ (domain databases like CDD) - - -Manual Installation -=================== - -For those not using Galaxy's automated installation from the Tool Shed, put -the XML and Python files in the tools/ncbi_blast_plus/ folder and add the XML -files to your tool_conf.xml as normal (and do the same in tool_conf.xml.sample -in order to run the unit tests). For example, use: - - <section name="NCBI BLAST+" id="ncbi_blast_plus_tools"> - <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastx_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_makeblastdb.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_blastdbcmd_info.xml" /> - <tool file="ncbi_blast_plus/ncbi_rpsblast_wrapper.xml" /> - <tool file="ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml" /> - <tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /> - </section> - -You will also need to install 'blast_datatypes' from the Tool Shed. This -defines the BLAST XML file format ('blastxml') and protein and nucleotide -BLAST databases composite file formats ('blastdbp' and 'blastdbn'). - -As described above for an automated installation, you must also tell Galaxy -about any system level BLAST databases using the tool-data/blastdb*.loc files. - -You must install the NCBI BLAST+ standalone tools somewhere on the system -path. Currently the unit tests are written using "BLAST 2.2.26+". - -Run the functional tests (adjusting the section identifier to match your -tool_conf.xml.sample file): - -./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools - - -History -======= - -v0.0.11 - Final revision as part of the Galaxy main repository, and the - first release via the Tool Shed -v0.0.12 - Implements genetic code option for translation searches. - - Changes <parallelism> to 1000 sequences at a time (to cope with - very large sets of queries where BLAST+ can become memory hungry) - - Include warning that BLAST+ with subject FASTA gives pairwise - e-values -v0.0.13 - Use the new error handling options in Galaxy (the previously - bundled hide_stderr.py script is no longer needed). -v0.0.14 - Support for makeblastdb and blastdbinfo with local BLAST databases - in the history (using work from Edward Kirton), requires v0.0.14 - of the 'blast_datatypes' repository from the Tool Shed. -v0.0.15 - Stronger warning in help text against searching against subject - FASTA files (better looking e-values than you might be expecting). -v0.0.16 - Added repository_dependencies.xml for automates installation of the - 'blast_datatypes' repository from the Tool Shed. -v0.0.17 - The BLAST+ search tools now default to extended tabular output - (all too often our users where having to re-run searches just to - get one of the missing columns like query or subject length) -v0.0.18 - Defensive quoting of filenames in case of spaces (where possible, - BLAST+ handling of some mult-file arguments is problematic). -v0.0.19 - Added wrappers for rpsblast and rpstblastn, and new blastdb_d.loc - for the domain databases they use (e.g. CDD, PFAM or SMART). - - Correct case of exception regular expression (for error handling - fall-back in case the return code is not set properly). - - Clearer naming of output files. - - -Developers -========== - -This script and related tools are being developed on the 'tools' branch of the -following Mercurial repository: -https://bitbucket.org/peterjc/galaxy-central/ - -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use -the following command from the Galaxy root folder: - -$ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh - -This simplifies ensuring a consistent set of files is bundled each time, -including all the relevant test files. - - -Licence (MIT/BSD style) -======================= - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. - -NOTE: This is the licence for the Galaxy Wrapper only. NCBI BLAST+ and -associated data files are available and licenced separately.
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.5"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.6"> <description>Show BLAST database information from blastdbcmd</description> <requirements> <requirement type="binary">blastdbcmd</requirement> @@ -57,9 +57,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.5"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.0.6"> <description>Extract sequence(s) from BLAST database</description> <requirements> <requirement type="binary">blastdbcmd</requirement> @@ -129,9 +129,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.19"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.20"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -37,6 +37,9 @@ #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -max_target_seqs $adv_opts.max_hits #end if +#if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): +-perc_identity $adv_opts.identity_cutoff +#end if #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if @@ -126,6 +129,7 @@ <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> <validator type="in_range" min="0" /> </param> + <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> <!-- I'd like word_size to be optional, with minimum 4 for blastn --> <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> <validator type="in_range" min="0" /> @@ -148,6 +152,18 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-40" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> + </test> + </tests> <help> .. class:: warningmark @@ -233,7 +249,20 @@ **References** -Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.19"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.20"> <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -298,9 +298,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -286,7 +286,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,5 +1,5 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.4"> - <description>Make BLAST database</description> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.5"> + <description>Make BLAST database</description> <requirements> <requirement type="binary">makeblastdb</requirement> <requirement type="package" version="2.2.26+">blast+</requirement> @@ -14,7 +14,8 @@ ## some extra spaces, e.g. -in " file1 file2 file3 " but BLAST seems happy: -in " #for $i in $in -${i.file} #end for +${i.file} +#end for " #if $title: -title "$title" @@ -38,71 +39,73 @@ ## #else if $tax.select == 'map': ## -taxid_map $tax.map ## #end if -</command> -<stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> -</stdio> -<inputs> - <param name="dbtype" type="select" display="radio" label="Molecule type of input"> - <option value="prot">protein</option> - <option value="nucl">nucleotide</option> - </param> - <!-- TODO Allow merging of existing BLAST databases (conditional on the database type) - <repeat name="in" title="Blast or Fasta Database" min="1"> - <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="Blast or Fasta database" /> - </repeat> - --> - <repeat name="in" title="FASTA file" min="1"> - <param name="file" type="data" format="fasta" /> - </repeat> - <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> - <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> - <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <inputs> + <param name="dbtype" type="select" display="radio" label="Molecule type of input"> + <option value="prot">protein</option> + <option value="nucl">nucleotide</option> + </param> + <!-- TODO Allow merging of existing BLAST databases (conditional on the database type) + <repeat name="in" title="BLAST or FASTA Database" min="1"> + <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="BLAST or FASTA database" /> + </repeat> + --> + <repeat name="in" title="FASTA file" min="1"> + <param name="file" type="data" format="fasta" /> + </repeat> + <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> + <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> + <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> - <!-- SEQUENCE MASKING OPTIONS --> - <!-- TODO - <repeat name="mask_data" title="Provide one or more files containing masking data"> - <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> - </repeat> - <repeat name="gi_mask" title="Create GI indexed masking data"> - <param name="file" type="data" format="asnb" label="Masking data output file" /> - </repeat> - --> + <!-- SEQUENCE MASKING OPTIONS --> + <!-- TODO + <repeat name="mask_data" title="Provide one or more files containing masking data"> + <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> + </repeat> + <repeat name="gi_mask" title="Create GI indexed masking data"> + <param name="file" type="data" format="asnb" label="Masking data output file" /> + </repeat> + --> - <!-- TAXONOMY OPTIONS --> - <!-- TODO - <conditional name="tax"> - <param name="select" type="select" label="Taxonomy options"> - <option value="">Do not assign sequences to Taxonomy IDs</option> - <option value="id">Assign all sequences to one Taxonomy ID</option> - <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> - </param> - <when value=""> - </when> - <when value="id"> - <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" /> - </when> - <when value="map"> - <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> - </when> - </conditional> - --> -</inputs> -<outputs> - <!-- If we only accepted one FASTA file, we could use its human name here... --> - <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> - <change_format> - <when input="dbtype" value="nucl" format="blastdbn"/> - <when input="dbtype" value="prot" format="blastdbp"/> - </change_format> - </data> -</outputs> -<help> + <!-- TAXONOMY OPTIONS --> + <!-- TODO + <conditional name="tax"> + <param name="select" type="select" label="Taxonomy options"> + <option value="">Do not assign sequences to Taxonomy IDs</option> + <option value="id">Assign all sequences to one Taxonomy ID</option> + <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> + </param> + <when value=""> + </when> + <when value="id"> + <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" /> + </when> + <when value="map"> + <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> + </when> + </conditional> + --> + </inputs> + <outputs> + <!-- If we only accepted one FASTA file, we could use its human name here... --> + <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> + <change_format> + <when input="dbtype" value="nucl" format="blastdbn" /> + <when input="dbtype" value="prot" format="blastdbp" /> + </change_format> + </data> + </outputs> + <tests> + </tests> + <help> **What it does** Make BLAST database from one or more FASTA files and/or BLAST databases. @@ -118,5 +121,23 @@ **Documentation** http://www.ncbi.nlm.nih.gov/books/NBK1763/ -</help> + +**References** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.3"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.0.4"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> @@ -230,7 +230,20 @@ **References** -Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.3"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.4"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> @@ -19,13 +19,13 @@ #end if -evalue $evalue_cutoff -out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected +## Set the extended list here so if/when we add things, saved workflows are not affected #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: -outfmt $out_format #end if -##Seems rpstblastn does not currently support multiple threads :( +## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+. ##-num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query @@ -231,7 +231,20 @@ **References** -Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.19"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.20"> <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -332,7 +332,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.19"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.20"> <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> @@ -190,6 +190,18 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-40" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="tblastx_rhodopsin_vs_three_human.tabular" ftype="tabular" /> + </test> + </tests> <help> .. class:: warningmark @@ -274,7 +286,20 @@ **References** -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 +Christiam Camacho et al. (2009). +BLAST+: architecture and applications. +BMC Bioinformatics. 15;10:421. +http://dx.doi.org/10.1186/1471-2105-10-421 + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus </help> </tool>
--- a/tools/ncbi_blast_plus/repository_dependencies.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,5 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> -<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases --> -<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> + <repository changeset_revision="b3a3ba0c1d47" name="blast_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </repositories>
--- a/tools/ncbi_blast_plus/tool_dependencies.xml Thu Apr 25 09:38:37 2013 -0400 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Mon Sep 23 06:14:13 2013 -0400 @@ -1,21 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="blast+" version="2.2.26+"> - <install version="1.0"> - <actions> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> - <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR && make && make install</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -These links provide information for building the NCBI Blast+ package in most environments. - -System requirements -http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download - </readme> + <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> -