# HG changeset patch
# User peterjc
# Date 1366206328 14400
# Node ID cf4903f5c81f975b7a3b90accf9dac411d907d55
# Parent b70b142bbc39cfd573d55850adfda102978777d9
Uploaded v0.0.17
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_four_human_vs_rhodopsin.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.tabular Wed Apr 17 09:45:28 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
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_four_human_vs_rhodopsin.xml
--- a/test-data/blastp_four_human_vs_rhodopsin.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,8 +1,8 @@
-
+
blastp
- BLASTP 2.2.25+
+ BLASTP 2.2.26+
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
@@ -375,7 +375,7 @@
1
- 701.049065538619
+ 701.049
1808
0
1
@@ -422,7 +422,7 @@
1
- 619.001555868222
+ 619.002
1595
0
1
@@ -469,7 +469,7 @@
1
- 653.284318124867
+ 653.284
1684
0
11
@@ -516,7 +516,7 @@
1
- 631.327942297578
+ 631.328
1627
0
11
@@ -563,7 +563,7 @@
1
- 673.314696072569
+ 673.315
1736
0
1
@@ -610,9 +610,9 @@
1
- 599.356377496438
+ 599.356
1544
- 3.49521227372659e-176
+ 0
1
341
1
@@ -643,4 +643,4 @@
-
+
\ No newline at end of file
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_four_human_vs_rhodopsin_ext.tabular
--- a/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:45:28 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
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastp_rhodopsin_vs_four_human.tabular
--- a/test-data/blastp_rhodopsin_vs_four_human.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastp_rhodopsin_vs_four_human.tabular Wed Apr 17 09:45:28 2013 -0400
@@ -1,6 +1,6 @@
gi|57163783|ref|NP_001009242.1| sp|P08100|OPSD_HUMAN 96.55 348 12 0 1 348 1 348 0.0 679
-gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 6e-178 605
+gi|3024260|sp|P56514.1|OPSD_BUFBU sp|P08100|OPSD_HUMAN 83.33 354 53 2 1 354 1 348 0.0 605
gi|283855846|gb|ADB45242.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630
gi|283855823|gb|ADB45229.1| sp|P08100|OPSD_HUMAN 94.82 328 17 0 1 328 11 338 0.0 630
gi|223523|prf||0811197A sp|P08100|OPSD_HUMAN 93.10 348 23 1 1 347 1 348 0.0 651
-gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 2e-172 587
+gi|12583665|dbj|BAB21486.1| sp|P08100|OPSD_HUMAN 81.09 349 65 1 1 349 1 348 0.0 587
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastx_rhodopsin_vs_four_human.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastx_rhodopsin_vs_four_human.tabular Wed Apr 17 09:45:28 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
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastx_rhodopsin_vs_four_human.xml
--- a/test-data/blastx_rhodopsin_vs_four_human.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastx_rhodopsin_vs_four_human.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,8 +1,8 @@
-
+
blastx
- BLASTX 2.2.25+
+ BLASTX 2.2.26+
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
@@ -90,7 +90,7 @@
1
- 662.143908370966
+ 662.144
1707
0
1
@@ -194,9 +194,9 @@
1
- 575.088804213644
+ 575.089
1481
- 1.31349806431671e-168
+ 0
42
1037
1
@@ -298,9 +298,9 @@
1
- 224.171990552935
+ 224.172
570
- 1.57574304751949e-62
+ 1.84906e-68
1
333
11
@@ -317,9 +317,9 @@
2
- 129.412894877266
+ 129.413
324
- 5.28220874623366e-34
+ 4.62305e-36
3174
3368
248
@@ -336,9 +336,9 @@
3
- 120.938504207085
+ 120.939
302
- 1.87871691987854e-31
+ 2.85192e-33
2855
3022
177
@@ -355,9 +355,9 @@
4
- 118.242107175663
+ 118.242
295
- 1.21774886471054e-30
+ 2.16231e-32
1404
1580
119
@@ -374,9 +374,9 @@
5
- 56.2249754529693
+ 56.225
134
- 5.68296036241677e-12
+ 2.05678e-12
4222
4296
312
@@ -478,9 +478,9 @@
1
- 613.993961381297
+ 613.994
1582
- 1.57028732393616e-180
+ 0
1
978
11
@@ -582,7 +582,7 @@
1
- 641.728330847346
+ 641.728
1654
0
1
@@ -686,9 +686,9 @@
1
- 559.295621601033
+ 559.296
1440
- 6.32632556748138e-164
+ 0
23
1018
1
@@ -719,4 +719,4 @@
-
+
\ No newline at end of file
diff -r b70b142bbc39 -r cf4903f5c81f test-data/blastx_rhodopsin_vs_four_human_ext.tabular
--- a/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/blastx_rhodopsin_vs_four_human_ext.tabular Wed Apr 17 09:45:28 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 1e-168 575 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-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 VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 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 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 6e-164 559 sp|P08100|OPSD_HUMAN 1440 272 307 0 92.47 2 0 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED 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 MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEED MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE 1344 348
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin.html
--- a/test-data/tblastn_four_human_vs_rhodopsin.html Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.html Wed Apr 17 09:45:28 2013 -0400
@@ -3,7 +3,7 @@
-TBLASTN 2.2.25+
+TBLASTN 2.2.26+
Query= sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44
@@ -563,7 +563,7 @@
Score = 151 bits (342), Expect(2) = 1e-72, Method: Compositional matrix adjust.
- Identities = 69/74 (94%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
+ Identities = 69/74 (93%), Positives = 73/74 (99%), Gaps = 0/74 (0%)
Frame = +3
Query 239 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA 298
@@ -584,8 +584,8 @@
Sbjct 2855 RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 3031
- Score = 229 bits (523), Expect = 1e-64, Method: Compositional matrix adjust.
- Identities = 107/111 (97%), Positives = 109/111 (99%), Gaps = 0/111 (0%)
+ Score = 229 bits (523), Expect = 9e-67, Method: Compositional matrix adjust.
+ Identities = 107/111 (96%), Positives = 109/111 (98%), Gaps = 0/111 (0%)
Frame = +1
Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70
@@ -598,7 +598,7 @@
Score = 122 bits (276), Expect = 1e-32, Method: Compositional matrix adjust.
- Identities = 55/59 (94%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
+ Identities = 55/59 (93%), Positives = 56/59 (95%), Gaps = 0/59 (0%)
Frame = +3
Query 119 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR 177
@@ -606,8 +606,8 @@
Sbjct 1404 LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 1580
- Score = 57.7 bits (125), Expect = 6e-13, Method: Compositional matrix adjust.
- Identities = 23/26 (89%), Positives = 24/26 (93%), Gaps = 0/26 (0%)
+ Score = 57.7 bits (125), Expect = 2e-12, Method: Compositional matrix adjust.
+ Identities = 23/26 (88%), Positives = 24/26 (92%), Gaps = 0/26 (0%)
Frame = +1
Query 312 QFRNCMLTTICCGKNPLGDDEASATV 337
@@ -637,7 +637,7 @@
Score = 658 bits (1517), Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 310/326 (96%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
+ Identities = 310/326 (95%), Positives = 322/326 (99%), Gaps = 0/326 (0%)
Frame = +1
Query 11 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT 70
@@ -687,7 +687,7 @@
Score = 711 bits (1640), Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 325/348 (94%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
+ Identities = 325/348 (93%), Positives = 337/348 (97%), Gaps = 0/348 (0%)
Frame = +1
Query 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
@@ -737,7 +737,7 @@
Score = 626 bits (1444), Expect = 0.0, Method: Compositional matrix adjust.
- Identities = 281/342 (83%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
+ Identities = 281/342 (82%), Positives = 311/342 (91%), Gaps = 1/342 (0%)
Frame = +2
Query 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.tabular Wed Apr 17 09:45:28 2013 -0400
@@ -2,9 +2,9 @@
sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646
sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151
sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64 229
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229
sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7
sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658
sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711
sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin.xml
--- a/test-data/tblastn_four_human_vs_rhodopsin.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,8 +1,8 @@
-
+
tblastn
- TBLASTN 2.2.25+
+ TBLASTN 2.2.26+
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
@@ -375,7 +375,7 @@
1
- 732.392902459534
+ 732.393
1689
0
1
@@ -422,7 +422,7 @@
1
- 646.119739014374
+ 646.12
1489
0
1
@@ -469,9 +469,9 @@
1
- 151.343146656381
+ 151.343
342
- 1.39566684546685e-72
+ 1.39567e-72
239
312
3147
@@ -488,9 +488,9 @@
2
- 126.323929257285
+ 126.324
284
- 1.39566684546685e-72
+ 1.39567e-72
177
235
2855
@@ -507,9 +507,9 @@
3
- 229.420359574251
+ 229.42
523
- 9.84654801241353e-65
+ 9.34154e-67
11
121
1
@@ -526,9 +526,9 @@
4
- 122.873002719478
+ 122.873
276
- 1.40732096096596e-32
+ 1.03783e-32
119
177
1404
@@ -545,9 +545,9 @@
5
- 57.7367643183824
+ 57.7368
125
- 5.60065526485586e-13
+ 1.50808e-12
312
337
4222
@@ -592,7 +592,7 @@
1
- 658.197981896696
+ 658.198
1517
0
11
@@ -639,7 +639,7 @@
1
- 711.255977415469
+ 711.256
1640
0
1
@@ -686,7 +686,7 @@
1
- 626.708277239213
+ 626.708
1444
0
1
@@ -719,4 +719,4 @@
-
+
\ No newline at end of file
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin_ext.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:44:44 2013 -0400
+++ b/test-data/tblastn_four_human_vs_rhodopsin_ext.tabular Wed Apr 17 09:45:28 2013 -0400
@@ -2,9 +2,9 @@
sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646 gi|2734705|gb|U59921.1|BBU59921 1489 290 320 1 93.57 0 3 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA-SATVSKTE MNGTEGPNFYIPMSNKTGVVRSPFEYPQYYLAEPWQYSILCAYMFLLILLGFPINFMTLYVTIQHKKLRTPLNYILLNLAFANHFMVLCGFTVTMYSSMNGYFILGATGCYVEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFSENHAVMGVAFTWIMALSCAVPPLLGWSRYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGRLVCTVKEAAAQQQESATTQKAEKEVTRMVIIMVVFFLICWVPYASVAFFIFSNQGSEFGPIFMTVPAFFAKSSSIYNPVIYIMLNKQFRNCMITTLCCGKNPFGEDDASSAATSKTE 348 1574
sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151 gi|283855845|gb|GQ290303.1| 342 69 73 0 98.65 0 3 ESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQ ESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSNFGPIFMTLPAFFAKSSSIYNPVIYIMMNKQ 348 4301
sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126 gi|283855845|gb|GQ290303.1| 284 54 57 0 96.61 0 2 RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAA RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEVRS 348 4301
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64 229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 9e-67 229 gi|283855845|gb|GQ290303.1| 523 107 109 0 98.20 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGG VPFSNKTGVVRSPFEHPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGG 348 4301
sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122 gi|283855845|gb|GQ290303.1| 276 55 56 0 94.92 0 3 LGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSR LAGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWSR 348 4301
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301
+sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 2e-12 57.7 gi|283855845|gb|GQ290303.1| 125 23 24 0 92.31 0 1 QFRNCMLTTICCGKNPLGDDEASATV QFRNCMLTTLCCGKNPLGDDEASTTA 348 4301
sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658 gi|283855822|gb|GQ290312.1| 1517 310 322 0 98.77 0 1 VPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASAT VPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVANLFMVFGGFTTTLYTSMHGYFVFGATGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLAFTWVMALACAAPPLAGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSNFGPVFMTIPAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDEASTT 348 983
sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711 gi|18148870|dbj|AB062417.1| 1640 325 337 0 96.84 0 1 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348 1047
sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626 gi|12583664|dbj|AB043817.1| 1444 281 311 1 90.94 0 2 MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE 348 1344
diff -r b70b142bbc39 -r cf4903f5c81f test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular
--- a/test-data/tblastn_four_human_vs_rhodopsin_parse_deflines.tabular Wed Apr 17 09:44:44 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-sp|P08100|OPSD_HUMAN gi|57163782|ref|NM_001009242.1| 96.55 348 12 0 1 348 1 1044 0.0 732
-sp|P08100|OPSD_HUMAN gi|2734705|gb|U59921.1|BBU59921 84.80 342 51 1 1 341 42 1067 0.0 646
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.24 74 5 0 239 312 3147 3368 1e-72 151
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 91.53 59 5 0 177 235 2855 3031 1e-72 126
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 96.40 111 4 0 11 121 1 333 1e-64 229
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 93.22 59 4 0 119 177 1404 1580 1e-32 122
-sp|P08100|OPSD_HUMAN gi|283855845|gb|GQ290303.1| 88.46 26 3 0 312 337 4222 4299 6e-13 57.7
-sp|P08100|OPSD_HUMAN gi|283855822|gb|GQ290312.1| 95.09 326 16 0 11 336 1 978 0.0 658
-sp|P08100|OPSD_HUMAN gi|18148870|dbj|AB062417.1| 93.39 348 23 0 1 348 1 1044 0.0 711
-sp|P08100|OPSD_HUMAN gi|12583664|dbj|AB043817.1| 82.16 342 60 1 1 341 23 1048 0.0 626
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/blastxml_to_tabular.xml
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,13 +1,18 @@
-
+
Convert BLAST XML output to tabular
blastxml_to_tabular.py $blastxml_file $tabular_file $out_format
+
+
+
+
+
-
-
+
+
@@ -74,7 +79,7 @@
may need both the XML and the tabular output - but running BLAST twice is
slow and wasteful.
-This tool takes the BLAST XML output and by default converts it into the
+This tool takes the BLAST XML output and can convert it into the
standard 12 column tabular equivalent:
====== ========= ============================================
@@ -99,7 +104,7 @@
included by selecting the extended tabular output. The extra columns are
included *after* the standard 12 columns. This is so that you can write
workflow filtering steps that accept either the 12 or 22 column tabular
-BLAST output.
+BLAST output. This tool now uses this extended 24 column output by default.
====== ============= ===========================================
Column NCBI name Description
@@ -121,7 +126,7 @@
Beware that the XML file (and thus the conversion) and the tabular output
direct from BLAST+ may differ in the presence of XXXX masking on regions
low complexity (columns 21 and 22), and thus also calculated figures like
-the percentage idenity (column 3).
+the percentage identity (column 3).
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blast_plus.txt
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Wed Apr 17 09:45:28 2013 -0400
@@ -34,7 +34,20 @@
For those not using Galaxy's automated installation from the Tool Shed, put
the XML and Python files under tools/ncbi_blast_plus and add the XML files
-to your tool_conf.xml as normal.
+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:
+
+
You will also need to install 'blast_datatypes' from the Tool Shed. This
defines the BLAST XML file format ('blastxml') and protein and nucleotide
@@ -45,6 +58,14 @@
databases like NR), located in the tool-data folder. Sample fils are included
which explain the tab based format to use.
+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 (adusting the section identifier to match your
+tool_conf.xml.sample file):
+
+./run_functional_tests.sh -sid NCBI_BLAST+-ncbi_blast_plus_tools
+
History
=======
@@ -65,6 +86,9 @@
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)
Developers
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,4 +1,4 @@
-
+
Search nucleotide database with nucleotide query sequence(s)
@@ -91,8 +91,8 @@
-
-
+
+
@@ -200,7 +200,7 @@
included by selecting the extended tabular output. The extra columns are
included *after* the standard 12 columns. This is so that you can write
workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
====== ============= ===========================================
Column NCBI name Description
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,4 +1,4 @@
-
+
Search protein database with protein query sequence(s)
@@ -86,8 +86,8 @@
-
-
+
+
@@ -265,7 +265,7 @@
included by selecting the extended tabular output. The extra columns are
included *after* the standard 12 columns. This is so that you can write
workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
====== ============= ===========================================
Column NCBI name Description
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,4 +1,4 @@
-
+
Search protein database with translated nucleotide query sequence(s)
@@ -103,8 +103,8 @@
-
-
+
+
@@ -253,7 +253,7 @@
included by selecting the extended tabular output. The extra columns are
included *after* the standard 12 columns. This is so that you can write
workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
====== ============= ===========================================
Column NCBI name Description
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,4 +1,4 @@
-
+
Search translated nucleotide database with protein query sequence(s)
@@ -82,8 +82,8 @@
-
-
+
+
@@ -216,7 +216,7 @@
-
+
@@ -299,7 +299,7 @@
included by selecting the extended tabular output. The extra columns are
included *after* the standard 12 columns. This is so that you can write
workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
====== ============= ===========================================
Column NCBI name Description
diff -r b70b142bbc39 -r cf4903f5c81f tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 09:44:44 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 09:45:28 2013 -0400
@@ -1,4 +1,4 @@
-
+
Search translated nucleotide database with translated nucleotide query sequence(s)
@@ -103,8 +103,8 @@
-
-
+
+
@@ -241,7 +241,7 @@
included by selecting the extended tabular output. The extra columns are
included *after* the standard 12 columns. This is so that you can write
workflow filtering steps that accept either the 12 or 24 column tabular
-BLAST output.
+BLAST output. Galaxy now uses this extended 24 column output by default.
====== ============= ===========================================
Column NCBI name Description