Difference between revisions of "GEvo Blastn Bug"
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− | ==Bug Description== | + | == Bug Description == |
− | + | ||
− | ==Visualization== | + | When using blastn in [[GEvo]], a large HSP appear in the middle of the region when the query sequence length is changed by 1 nucleotide. |
− | Difference between analyses is that addition of 1 nucleotide to the top panel of the top analysis | + | |
− | [[ | + | == Visualization == |
− | [[ | + | |
+ | Difference between analyses is that addition of 1 nucleotide to the top panel of the top analysis [[Image:Screen Shot 2012-02-11 at 4.55.25 AM.png|thumb|center|500px]] [[Image:Screen Shot 2012-02-11 at 4.57.06 AM.png|thumb|center|500px]] | ||
+ | |||
+ | == Report of "disappearing" HSP in blast file == | ||
+ | |||
+ | Top portion of blast report which contains the large HSP:<br> | ||
+ | <pre>BLASTN 2.2.24+ | ||
+ | |||
+ | Query= AT1G75520 | ||
+ | Length=478 | ||
+ | |||
+ | Subject= Bra008203 | ||
+ | Length=17361 | ||
+ | |||
+ | |||
+ | Score = 68.0 bits (35), Expect = 3e-14 | ||
+ | Identities = 76/94 (80%), Gaps = 4/94 (4%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | Query 1 CTAGGTTTCGTGTTCCACTGATCAAAGATTTGAAAAAAAACATATACTTAGTAAACTTCA 60 | ||
+ | |||||||| ||||||||||||||||||| || || ||||||| | |||||| | | ||
+ | Sbjct 9943 CTAGGTTTTGTGTTCCACTGATCAAAGAGTT----AAGAACATATTTCAATAAAACTTTA 9998 | ||
+ | |||
+ | Query 61 AGCAATTTTTATATTACCCAATTGAATTTCTCCA 94 | ||
+ | | |||||||||| |||||| ||||||||||||| | ||
+ | Sbjct 9999 AATAATTTTTATACTACCCAGTTGAATTTCTCCA 10032 | ||
+ | |||
+ | |||
+ | Score = 54.5 bits (28), Expect = 3e-10 | ||
+ | Identities = 32/34 (94%), Gaps = 0/34 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | Query 442 TTGGCGTAGATGAATGTAAACGGATGGTAATATA 475 | ||
+ | |||||||| |||||||||||||||| |||||||| | ||
+ | Sbjct 10342 TTGGCGTATATGAATGTAAACGGATAGTAATATA 10375 | ||
+ | |||
+ | |||
+ | Score = 50.7 bits (26), Expect = 4e-09 | ||
+ | Identities = 77/95 (81%), Gaps = 5/95 (5%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | Query 129 ATATATATATACCCAACAACTGAGAAAAGATGGAAAAAGTTTAGTTAAAAACTGGTCCTG 188 | ||
+ | ||||||||||| |||||| || |||||||||||| || || ||||||||| | | | ||
+ | Sbjct 10072 ATATATATATAACCAACATCTCGGAAAAGATGGAACAAATT-AGTTAAAAAAA---CATT 10127 | ||
+ | |||
+ | Query 189 GGCGGCTTTAAATTATATTTATGCACTTAAATTTA 223 | ||
+ | ||||||||||||| ||||| ||| | ||||||||| | ||
+ | Sbjct 10128 GGCGGCTTTAAATCATATTCATGTA-TTAAATTTA 10161 | ||
+ | |||
+ | |||
+ | Score = 48.8 bits (25), Expect = 2e-08 | ||
+ | Identities = 47/58 (81%), Gaps = 0/58 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | Query 316 GGTTTTTACTTAGATAATATCGTGTCATTCCATCTAGATTCAACCCCTGTCTACAATA 373 | ||
+ | |||||| ||| |||| |||| || || | | ||||||||||||||| ||||||||| | ||
+ | Sbjct 10207 GGTTTTCACTGAGATGATATTGTTCCAGTTCCACTAGATTCAACCCCTCTCTACAATA 10264 | ||
+ | |||
+ | |||
+ | Score = 25.7 bits (13), Expect = 0.15 | ||
+ | Identities = 13/13 (100%), Gaps = 0/13 (0%) | ||
+ | Strand=Plus/Plus | ||
+ | |||
+ | Query 127 TAATATATATATA 139 | ||
+ | ||||||||||||| | ||
+ | Sbjct 7327 TAATATATATATA 7339 | ||
+ | |||
+ | </pre> |
Revision as of 06:00, 11 February 2012
Bug Description
When using blastn in GEvo, a large HSP appear in the middle of the region when the query sequence length is changed by 1 nucleotide.
Visualization
Difference between analyses is that addition of 1 nucleotide to the top panel of the top analysisReport of "disappearing" HSP in blast file
Top portion of blast report which contains the large HSP:
BLASTN 2.2.24+ Query= AT1G75520 Length=478 Subject= Bra008203 Length=17361 Score = 68.0 bits (35), Expect = 3e-14 Identities = 76/94 (80%), Gaps = 4/94 (4%) Strand=Plus/Plus Query 1 CTAGGTTTCGTGTTCCACTGATCAAAGATTTGAAAAAAAACATATACTTAGTAAACTTCA 60 |||||||| ||||||||||||||||||| || || ||||||| | |||||| | Sbjct 9943 CTAGGTTTTGTGTTCCACTGATCAAAGAGTT----AAGAACATATTTCAATAAAACTTTA 9998 Query 61 AGCAATTTTTATATTACCCAATTGAATTTCTCCA 94 | |||||||||| |||||| ||||||||||||| Sbjct 9999 AATAATTTTTATACTACCCAGTTGAATTTCTCCA 10032 Score = 54.5 bits (28), Expect = 3e-10 Identities = 32/34 (94%), Gaps = 0/34 (0%) Strand=Plus/Plus Query 442 TTGGCGTAGATGAATGTAAACGGATGGTAATATA 475 |||||||| |||||||||||||||| |||||||| Sbjct 10342 TTGGCGTATATGAATGTAAACGGATAGTAATATA 10375 Score = 50.7 bits (26), Expect = 4e-09 Identities = 77/95 (81%), Gaps = 5/95 (5%) Strand=Plus/Plus Query 129 ATATATATATACCCAACAACTGAGAAAAGATGGAAAAAGTTTAGTTAAAAACTGGTCCTG 188 ||||||||||| |||||| || |||||||||||| || || ||||||||| | | Sbjct 10072 ATATATATATAACCAACATCTCGGAAAAGATGGAACAAATT-AGTTAAAAAAA---CATT 10127 Query 189 GGCGGCTTTAAATTATATTTATGCACTTAAATTTA 223 ||||||||||||| ||||| ||| | ||||||||| Sbjct 10128 GGCGGCTTTAAATCATATTCATGTA-TTAAATTTA 10161 Score = 48.8 bits (25), Expect = 2e-08 Identities = 47/58 (81%), Gaps = 0/58 (0%) Strand=Plus/Plus Query 316 GGTTTTTACTTAGATAATATCGTGTCATTCCATCTAGATTCAACCCCTGTCTACAATA 373 |||||| ||| |||| |||| || || | | ||||||||||||||| ||||||||| Sbjct 10207 GGTTTTCACTGAGATGATATTGTTCCAGTTCCACTAGATTCAACCCCTCTCTACAATA 10264 Score = 25.7 bits (13), Expect = 0.15 Identities = 13/13 (100%), Gaps = 0/13 (0%) Strand=Plus/Plus Query 127 TAATATATATATA 139 ||||||||||||| Sbjct 7327 TAATATATATATA 7339