# HG changeset patch # User peterjc # Date 1381223306 14400 # Node ID 5ec998a3530c0c85a489d05a3cd5149e99d176a4 # Parent aecdffbc08fc35ec3034bfba0f6024477294f21a Uploaded v0.0.21, includes support for masking, uses macros internally, and now targets BLAST+ 2.2.27 rather than BLAST+ 2.2.26 diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastn_rhodopsin_vs_three_human.tabular --- a/test-data/blastn_rhodopsin_vs_three_human.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastn_rhodopsin_vs_three_human.tabular Tue Oct 08 05:08:26 2013 -0400 @@ -1,7 +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|57163782|ref|NM_001009242.1| ENA|BC112106|BC112106.1 92.07 1047 83 0 1 1047 88 1134 0.0 1474 gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 91.59 333 28 0 1 333 118 450 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 +gi|283855845|gb|GQ290303.1| ENA|BC112106|BC112106.1 92.94 170 12 0 2854 3023 615 784 8e-69 248 +gi|283855822|gb|GQ290312.1| ENA|BC112106|BC112106.1 91.55 959 81 0 1 959 118 1076 0.0 1323 +gi|18148870|dbj|AB062417.1| ENA|BC112106|BC112106.1 87.50 1048 129 2 1 1047 88 1134 0.0 1208 diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Tue Oct 08 05:08:26 2013 -0400 @@ -2,7 +2,7 @@ blastp - BLASTP 2.2.26+ + BLASTP 2.2.27+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. sp|Q9BS26|ERP44_HUMAN diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human.tabular --- a/test-data/blastx_rhodopsin_vs_four_human.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Tue Oct 08 05:08:26 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 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 0.0 559 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Tue Oct 08 05:08:26 2013 -0400 @@ -2,7 +2,7 @@ blastx - BLASTX 2.2.26+ + BLASTX 2.2.27+ Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query_1 @@ -28,8 +28,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -47,8 +47,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -66,8 +66,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -90,8 +90,8 @@ 1 - 662.144 - 1707 + 639.032 + 1647 0

1044 @@ -114,8 +114,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -132,8 +132,8 @@

0 - 32 - 155472 + 33 + 183143 0.041 0.267 0.14 @@ -151,8 +151,8 @@

0 - 32 - 155472 + 33 + 183143 0.041 0.267 0.14 @@ -170,8 +170,8 @@

0 - 32 - 155472 + 33 + 183143 0.041 0.267 0.14 @@ -194,8 +194,8 @@ 1 - 575.089 - 1481 + 551.206 + 1419 0

1037 @@ -218,8 +218,8 @@

0 - 32 - 155472 + 33 + 183143 0.041 0.267 0.14 @@ -236,8 +236,8 @@

0 - 39 - 430746 + 40 + 509838 0.041 0.267 0.14 @@ -255,8 +255,8 @@

0 - 39 - 430746 + 40 + 509838 0.041 0.267 0.14 @@ -274,8 +274,8 @@

0 - 39 - 430746 + 40 + 509838 0.041 0.267 0.14 @@ -298,9 +298,9 @@ 1 - 224.172 - 570 - 1.84906e-68 + 220.32 + 560 + 4.29169e-67

333

11 @@ -317,9 +317,9 @@ 2 - 129.413 - 324 - 4.62305e-36 + 127.487 + 319 + 1.95079e-35

3174

3368

248 @@ -336,28 +336,28 @@ 3 - 120.939 - 302 - 2.85192e-33 + 121.324 + 303 + 1.96633e-33 2855 - 3022 + 3031 177 - 232 + 235

54 - 56 + 57 0 - 56 - RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKE - RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKE - RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE + 59 + RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS + RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA + RYIPEG+QCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKE + 4 - 118.242 - 295 - 2.16231e-32 + 97.0561 + 240 + 1.16473e-25

1404

1580

119 @@ -374,22 +374,22 @@ 5 - 56.225 - 134 - 2.05678e-12 + 56.9954 + 136 + 1.23645e-12 4222 - 4296 + 4299 312 - 336 + 337

23 24 0 - 25 - QFRNCMLTTLCCGKNPLGDDEASTT - QFRNCMLTTICCGKNPLGDDEASAT - QFRNCMLTT+CCGKNPLGDDEAS T + 26 + QFRNCMLTTLCCGKNPLGDDEASTTA + QFRNCMLTTICCGKNPLGDDEASATV + QFRNCMLTT+CCGKNPLGDDEAS T @@ -398,8 +398,8 @@

0 - 39 - 430746 + 40 + 509838 0.041 0.267 0.14 @@ -416,8 +416,8 @@

0 - 28 - 95680 + 29 + 112346 0.041 0.267 0.14 @@ -435,8 +435,8 @@

0 - 28 - 95680 + 29 + 112346 0.041 0.267 0.14 @@ -454,8 +454,8 @@

0 - 28 - 95680 + 29 + 112346 0.041 0.267 0.14 @@ -478,8 +478,8 @@ 1 - 613.994 - 1582 + 589.341 + 1518 0

978 @@ -502,8 +502,8 @@

0 - 28 - 95680 + 29 + 112346 0.041 0.267 0.14 @@ -520,8 +520,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -539,8 +539,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -558,8 +558,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -582,8 +582,8 @@ 1 - 641.728 - 1654 + 619.387 + 1596 0

1044 @@ -606,8 +606,8 @@

0 - 29 - 102080 + 30 + 119944 0.041 0.267 0.14 @@ -624,8 +624,8 @@

0 - 31 - 132189 + 32 + 155584 0.041 0.267 0.14 @@ -643,8 +643,8 @@

0 - 31 - 132189 + 32 + 155584 0.041 0.267 0.14 @@ -662,8 +662,8 @@

0 - 31 - 132189 + 32 + 155584 0.041 0.267 0.14 @@ -686,22 +686,22 @@ 1 - 559.296 - 1440 + 532.717 + 1371 0 23 - 1018 + 1021 1 - 332 + 333

272 307 0 - 332 - MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED - MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE - MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++ + 333 + MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG + MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA + MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++ @@ -710,8 +710,8 @@

0 - 31 - 132189 + 32 + 155584 0.041 0.267 0.14 diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human_converted.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted.tabular Tue Oct 08 05:08:26 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 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 0.0 559 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 92.31 65 5 0 3174 3368 248 312 2e-35 127 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_converted_ext.tabular Tue Oct 08 05:08:26 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 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 0.0 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 sp|P08100|OPSD_HUMAN 560 107 109 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 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 303 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVXXXXXXXXXXXXXXXXXKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 diff -r aecdffbc08fc -r 5ec998a3530c test-data/blastx_rhodopsin_vs_four_human_ext.tabular --- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Tue Oct 08 05:08:26 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 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 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 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD 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 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 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 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 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 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348 +gi|57163782|ref|NM_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 1044 1 348 0.0 639 sp|P08100|OPSD_HUMAN 1647 336 343 0 98.56 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTTGSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 +gi|2734705|gb|U59921.1|BBU59921 sp|P08100|OPSD_HUMAN 85.24 332 49 0 42 1037 1 332 0.0 551 sp|P08100|OPSD_HUMAN 1419 283 315 0 94.88 3 0 MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDD MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1574 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 96.40 111 4 0 1 333 11 121 4e-67 220 sp|P08100|OPSD_HUMAN 560 107 109 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 2e-35 127 sp|P08100|OPSD_HUMAN 319 60 64 0 98.46 3 0 KEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ KEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 91.53 59 5 0 2855 3031 177 235 2e-33 121 sp|P08100|OPSD_HUMAN 303 54 57 0 96.61 2 0 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 93.22 59 4 0 1404 1580 119 177 1e-25 97.1 sp|P08100|OPSD_HUMAN 240 55 56 0 94.92 3 0 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 4301 348 +gi|283855845|gb|GQ290303.1| sp|P08100|OPSD_HUMAN 88.46 26 3 0 4222 4299 312 337 1e-12 57.0 sp|P08100|OPSD_HUMAN 136 23 24 0 92.31 1 0 QFRNCMLTTLCCGKNPLGDDEASTTA QFRNCMLTTICCGKNPLGDDEASATV 4301 348 +gi|283855822|gb|GQ290312.1| sp|P08100|OPSD_HUMAN 95.09 326 16 0 1 978 11 336 0.0 589 sp|P08100|OPSD_HUMAN 1518 310 322 0 98.77 1 0 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT 983 348 +gi|18148870|dbj|AB062417.1| sp|P08100|OPSD_HUMAN 93.39 348 23 0 1 1044 1 348 0.0 619 sp|P08100|OPSD_HUMAN 1596 325 337 0 96.84 1 0 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA 1047 348 +gi|12583664|dbj|AB043817.1| sp|P08100|OPSD_HUMAN 81.68 333 61 0 23 1021 1 333 0.0 532 sp|P08100|OPSD_HUMAN 1371 272 307 0 92.19 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA 1344 348 diff -r aecdffbc08fc -r 5ec998a3530c test-data/dustmasker_three_human.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.fasta Tue Oct 08 05:08:26 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 diff -r aecdffbc08fc -r 5ec998a3530c test-data/dustmasker_three_human.maskinfo-asn1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dustmasker_three_human.maskinfo-asn1 Tue Oct 08 05:08:26 2013 -0400 @@ -0,0 +1,64 @@ +Blast-db-mask-info ::= { + algo-id 2, + algo-program dust, + algo-options "window=64; level=20; linker=1", + masks { + masks { + packed-int { + { + from 1447, + to 1495, + id local id 1 + }, + { + from 1540, + to 1552, + id local id 1 + }, + { + from 1886, + to 1892, + id local id 1 + }, + { + from 2278, + to 2284, + id local id 1 + }, + { + from 4409, + to 4415, + id local id 1 + }, + { + from 4635, + to 4653, + id local id 1 + }, + { + from 4726, + to 4734, + id local id 1 + } + }, + packed-int { + { + from 139, + to 219, + id local id 2 + }, + { + from 4569, + to 4584, + id local id 2 + }, + { + from 4621, + to 4648, + id local id 2 + } + } + }, + more FALSE + } +} diff -r aecdffbc08fc -r 5ec998a3530c test-data/dustmasker_three_human.maskinfo-asn1-binary Binary file test-data/dustmasker_three_human.maskinfo-asn1-binary has changed diff -r aecdffbc08fc -r 5ec998a3530c test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Sep 23 06:13:22 2013 -0400 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Tue Oct 08 05:08:26 2013 -0400 @@ -3,7 +3,7 @@

 
-TBLASTN 2.2.26+
+TBLASTN 2.2.27+
 
 
 Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
@@ -20,12 +20,12 @@
 
 
 
-Lambda     K      H
-   0.347    0.182    0.684 
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 127710
 
@@ -45,12 +45,12 @@
 
 
 
-Lambda     K      H
-   0.347    0.182    0.684 
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 127710
 
@@ -70,12 +70,12 @@
 
 
 
-Lambda     K      H
-   0.347    0.182    0.684 
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 127710
 
@@ -95,12 +95,12 @@
 
 
 
-Lambda     K      H
-   0.347    0.182    0.684 
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 127710
 
@@ -120,12 +120,12 @@
 
 
 
-Lambda     K      H
-   0.347    0.182    0.684 
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 127710
 
@@ -145,12 +145,12 @@
 
 
 
-Lambda     K      H
-   0.347    0.182    0.684 
+Lambda      K        H        a         alpha
+   0.347    0.182    0.684    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 127710
 
@@ -169,12 +169,12 @@
 
 
 
-Lambda     K      H
-   0.334    0.170    0.615 
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 370988
 
@@ -194,12 +194,12 @@
 
 
 
-Lambda     K      H
-   0.334    0.170    0.615 
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 370988
 
@@ -219,12 +219,12 @@
 
 
 
-Lambda     K      H
-   0.334    0.170    0.615 
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 370988
 
@@ -244,12 +244,12 @@
 
 
 
-Lambda     K      H
-   0.334    0.170    0.615 
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 370988
 
@@ -269,12 +269,12 @@
 
 
 
-Lambda     K      H
-   0.334    0.170    0.615 
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 370988
 
@@ -294,12 +294,12 @@
 
 
 
-Lambda     K      H
-   0.334    0.170    0.615 
+Lambda      K        H        a         alpha
+   0.334    0.170    0.615    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 370988
 
@@ -318,12 +318,12 @@
 
 
 
-Lambda     K      H
-   0.346    0.180    0.700 
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 441350
 
@@ -343,12 +343,12 @@
 
 
 
-Lambda     K      H
-   0.346    0.180    0.700 
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 441350
 
@@ -368,12 +368,12 @@
 
 
 
-Lambda     K      H
-   0.346    0.180    0.700 
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 441350
 
@@ -393,12 +393,12 @@
 
 
 
-Lambda     K      H
-   0.346    0.180    0.700 
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 441350
 
@@ -418,12 +418,12 @@
 
 
 
-Lambda     K      H
-   0.346    0.180    0.700 
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 441350
 
@@ -443,12 +443,12 @@
 
 
 
-Lambda     K      H
-   0.346    0.180    0.700 
+Lambda      K        H        a         alpha
+   0.346    0.180    0.700    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 441350
 
@@ -492,12 +492,12 @@
 
 
 
-Lambda     K      H
-   0.351    0.182    0.707 
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 109230
 
@@ -542,12 +542,12 @@
 
 
 
-Lambda     K      H
-   0.351    0.182    0.707 
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 109230
 
@@ -616,12 +616,12 @@
 
 
 
-Lambda     K      H
-   0.351    0.182    0.707 
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 109230
 
@@ -666,12 +666,12 @@
 
 
 
-Lambda     K      H
-   0.351    0.182    0.707 
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 109230
 
@@ -716,12 +716,12 @@
 
 
 
-Lambda     K      H
-   0.351    0.182    0.707 
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 109230
 
@@ -766,12 +766,12 @@
 
 
 
-Lambda     K      H
-   0.351    0.182    0.707 
+Lambda      K        H        a         alpha
+   0.351    0.182    0.707    0.522     1.92 
 
 Gapped
-Lambda     K      H
-   0.299   0.0710    0.270 
+Lambda      K        H        a         alpha    sigma
+   0.299   0.0710    0.270     1.10     13.8     14.5 
 
 Effective search space used: 109230
 
diff -r aecdffbc08fc -r 5ec998a3530c test-data/tblastn_four_human_vs_rhodopsin.xml
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -2,7 +2,7 @@
 
 
   tblastn
-  TBLASTN 2.2.26+
+  TBLASTN 2.2.27+
   Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
   
   Query_1
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/README.rst
--- a/tools/ncbi_blast_plus/README.rst	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Tue Oct 08 05:08:26 2013 -0400
@@ -53,6 +53,7 @@
     
     
     
+    
     
     
     
@@ -62,7 +63,9 @@
 
 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').
+BLAST databases composite file formats ('blastdbp' and 'blastdbn'):
+
+* http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
 
 As described above for an automated installation, you must also tell Galaxy
 about any system level BLAST databases using the tool-data/blastdb*.loc files.
@@ -117,6 +120,13 @@
         - Adopted standard MIT License.
         - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
         - Updated citation information (Cock et al. 2013).
+v0.0.21 - Use macros to simplify the XML wrappers.
+        - Added wrapper for dustmasker
+        - Enabled masking for makeblastdb
+        - Requires 'maskinfo-asn1' and 'maskinfo-asn1-binary' datatypes
+          defined in updated blast_datatypes on Galaxy ToolShed.
+        - Tests updated for BLAST+ 2.2.27 instead of BLAST+ 2.2.26
+        - Now depends on package_blast_plus_2_2_27 in ToolShed
 ======= ======================================================================
 
 
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,46 +1,19 @@
-
+
     Show BLAST database information from blastdbcmd
     
         blastdbcmd
-        blast+
+        blast+
     
     blastdbcmd -version
+    
+        ncbi_macros.xml
+    
     
 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out "$info"
     
-    
-        
-        
-        
-	
-	
-	
-    
+    
     
-        
-            
-              
-              
-            
-            
-                
-                    
-                      
-                      
-                      
-                    
-                
-            
-            
-                
-                    
-                      
-                      
-                      
-                    
-                
-            
-        
+        
     
     
         
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,10 +1,13 @@
-
+
     Extract sequence(s) from BLAST database
     
         blastdbcmd
-        blast+
+        blast+
     
     blastdbcmd -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -47,39 +50,9 @@
 | sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
 #end if
     
-    
-        
-        
-        
-	
-	
-	
-    
+    
     
-        
-            
-              
-              
-            
-            
-                
-                    
-                      
-                      
-                      
-                    
-                
-            
-            
-                
-                    
-                      
-                      
-                      
-                    
-                
-            
-        
+        
         
             
               
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,12 +1,15 @@
-
+
     Search nucleotide database with nucleotide query sequence(s)
     
     
     
         blastn
-        blast+
+        blast+
     
     blastn -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -48,44 +51,14 @@
 ## End of advanced options:
 #end if
     
-    
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+
+    
+
     
          
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+
+        
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@@ -97,20 +70,7 @@
             -->
         
         
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@@ -141,15 +101,7 @@
     
     
         
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+            
         
     
     
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,12 +1,15 @@
-
+
     Search protein database with protein query sequence(s)
     
     
     
         blastp
-        blast+
+        blast+
     
     blastp -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -46,63 +49,20 @@
 ## End of advanced options:
 #end if
     
-    
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+    
+
     
          
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@@ -112,16 +72,9 @@
             
                 
                 
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+                
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@@ -142,15 +95,7 @@
     
     
         
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+            
         
     
     
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,12 +1,15 @@
-
+
     Search protein database with translated nucleotide query sequence(s)
     
     
     
         blastx
-        blast+
+        blast+
     
     blastx -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -46,80 +49,18 @@
 ## End of advanced options:
 #end if
     
-    
-        
-        
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-        
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-    
+
+    
+
     
          
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+        
+        
         
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+        
+
         
             
               
@@ -134,16 +75,9 @@
                     
                     
                 
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+
+                
+
                 
                 
                     
@@ -159,15 +93,7 @@
     
     
         
-            
-                
-                
-                
-                
-                
-                
-                
-            
+            
         
     
     
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -0,0 +1,115 @@
+
+    
+    masks low complexity regions
+    
+        dustmasker
+        blast+
+    
+    dustmasker -version-full
+    
+        ncbi_macros.xml
+    
+    
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+dustmasker
+#if $db_opts.db_opts_selector == "db":
+  -in "${db_opts.database.fields.path}" -infmt blastdb
+#elif $db_opts.db_opts_selector == "histdb":
+  -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb
+#else:
+  -in "$subject" -infmt fasta
+#end if
+-out "$outfile"
+-window $window -level $level -linker $linker -outfmt $outformat
+    
+    
+    
+        
+        
+        
+        
+        
+
+
+            
+            
+            
+            
+
+        
+    
+    
+        
+            
+                
+                
+                
+            
+        
+    
+    
+        
+            
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+            
+            
+        
+    
+    
+**What it does**
+
+This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST algorithm.
+
+If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool.
+
+More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_.
+
+.. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers (a more specific paper covering this wrapper is planned):
+
+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
+    
+
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -0,0 +1,220 @@
+
+    
+
+        
+            
+            
+            
+            
+            
+            
+            
+        
+
+    
+    
+        
+            
+            
+            
+            
+            
+            
+            
+            
+            
+            
+        
+    
+    
+        
+            
+            
+            
+             
+            
+            
+            
+            
+        
+    
+    
+        
+            
+            
+            
+            
+            
+            
+        
+    
+    
+        
+            
+            
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+            
+        
+    
+
+    
+        
+            
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+            
+            
+            
+        
+    
+
+    
+        
+            
+              
+              
+              
+            
+            
+                
+                    
+                      
+                      
+                      
+                    
+                
+                
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+            
+            
+                
+                
+                
+            
+            
+                
+                
+                 
+            
+        
+    
+
+    
+        
+            
+              
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+              
+            
+            
+                
+                    
+                      
+                      
+                      
+                    
+                
+                
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+            
+            
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+                
+                
+            
+            
+                
+                
+                 
+            
+        
+    
+
+    
+        
+            
+              
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+            
+            
+                
+                    
+                      
+                      
+                      
+                    
+                
+                
+                
+            
+            
+        
+    
+
+    
+        
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+                
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+        
+    
+
+
+
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,10 +1,13 @@
-
+
     Make BLAST database
     
         makeblastdb
-        blast+
+        blast+
     
     makeblastdb -version
+    
+        ncbi_macros.xml
+    
     
 makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}"
 $parse_seqids
@@ -24,30 +27,29 @@
 -title "BLAST Database"
 #end if
 -dbtype $dbtype 
-## #set $sep = '-mask_data '
-## #for $i in $mask_data
-## $sep${i.file}
-## #set $set = ', '
-## #end for 
+#set $mask_string = ''
+#set $sep = '-mask_data '
+#for $i in $mask_data
+#set $mask_string += $sep + str($i.file)
+#set $sep = ','
+#end for
+$mask_string
+## #set $gi_mask_string = ''
 ## #set $sep = '-gi_mask -gi_mask_name '
 ## #for $i in $gi_mask
-## $sep${i.file}
-## #set $set = ', '
-## #end for 
+## #set $gi_mask_string += $sep + str($i.file)
+## #set $sep = ','
+## #end for
+## $gi_mask_string
 ## #if $tax.select == 'id':
 ## -taxid $tax.id
 ## #else if $tax.select == 'map':
 ## -taxid_map $tax.map
 ## #end if
     
-    
-        
-        
-        
-        
-        
-        
-    
+
+    
+
     
         
             
@@ -66,10 +68,10 @@
         
 
         
+        
+            
+        
         
     
     
         rpsblast
-        blast+
+        blast+
     
     rpsblast -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -40,57 +43,18 @@
 ## End of advanced options:
 #end if
     
-    
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+
+    
+
     
          
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@@ -114,15 +78,9 @@
     
     
         
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+
+            
+
         
     
     
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,12 +1,15 @@
-
+
     Search protein domain database (PSSMs) with translated nucleotide query sequence(s)
     
     
     
         rpstblastn
-        blast+
+        blast+
     
     rpstblastn -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -41,57 +44,16 @@
 ## End of advanced options:
 #end if
     
-    
-        
-        
-        
-        
-        
-        
-    
+    
     
          
-        
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+
+        
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+
+        
+
         
             
               
@@ -115,15 +77,7 @@
     
     
         
-            
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-                
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-                
-                
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+            
         
     
     
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,12 +1,15 @@
-
+
     Search translated nucleotide database with protein query sequence(s)
     
     
     
         tblastn
-        blast+
+        blast+
     
     tblastn -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -46,59 +49,16 @@
 ## End of advanced options:
 #end if
     
-    
-        
-        
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-    
+
+    
+
     
          
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+
         
             
               
@@ -106,39 +66,14 @@
             
             
             
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@@ -159,15 +94,7 @@
     
     
         
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+            
         
     
     
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,12 +1,15 @@
-
+
     Search translated nucleotide database with translated nucleotide query sequence(s)
     
     
     
         tblastx
-        blast+
+        blast+
     
     tblastx -version
+    
+        ncbi_macros.xml
+    
     
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
@@ -46,80 +49,18 @@
 ## End of advanced options:
 #end if
     
-    
-        
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+
+    
+
     
          
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@@ -127,27 +68,9 @@
             
             
             
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@@ -155,16 +78,7 @@
                     
                     
                 
-                
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@@ -179,15 +93,7 @@
     
     
         
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+            
         
     
     
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/repository_dependencies.xml
--- a/tools/ncbi_blast_plus/repository_dependencies.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/repository_dependencies.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,4 +1,4 @@
 
 
-    
+    
 
diff -r aecdffbc08fc -r 5ec998a3530c tools/ncbi_blast_plus/tool_dependencies.xml
--- a/tools/ncbi_blast_plus/tool_dependencies.xml	Mon Sep 23 06:13:22 2013 -0400
+++ b/tools/ncbi_blast_plus/tool_dependencies.xml	Tue Oct 08 05:08:26 2013 -0400
@@ -1,6 +1,6 @@
 
 
-    
-        
+    
+