[Bioperl-l] Difference between
Wiepert, Mathieu
Wiepert.Mathieu at mayo.edu
Tue Feb 3 09:49:49 EST 2004
Hi,
When I reported this, I was told that it was actually a minor bug, and they would look into it. It didn't sound like something they were going to address any time soon, and I never followed up, so guess it is still the same issue...
-mat
> -----Original Message-----
> From: Alan Li [mailto:immunoguest at hotmail.com]
> Sent: Saturday, January 31, 2004 5:26 PM
> To: Wiepert, Mathieu; bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Difference between
>
>
> I would like to thank everyone for their responses.
>
> And yes, Mat is right about this being an issue with the XML
> output of
> stand-alone blast. I tried comparing the results of just the
> stand-alone
> blast using different -F flags. The results below shows that
> if "-F F" is
> set the results are the same, but are different when using
> "-F T" for the
> XML output.
>
> So is there anything I could do to make the XML results the
> same when the
> filtering option is set to true? Perhaps either through
> another blast
> parameter or by doing it programmatically?
>
> --------------------------------------------------------------
> ---------
>
> blastall -p blastn -m 7 -F T -d ecoli/ecoli.nt -i test.txt
>
> <Hit>
> <Hit_num>1</Hit_num>
> <Hit_id>gi|1786181|gb|AE000111.1|AE000111</Hit_id>
> <Hit_def>Escherichia coli K-12 MG1655 section 1 of
> 400 of the
> complete genome</Hit_def>
> <Hit_accession>AE000111</Hit_accession>
> <Hit_len>10596</Hit_len>
> <Hit_hsps>
> <Hsp>
> <Hsp_num>1</Hsp_num>
> <Hsp_bit-score>589.253</Hsp_bit-score>
> <Hsp_score>297</Hsp_score>
> <Hsp_evalue>1.04898e-168</Hsp_evalue>
> <Hsp_query-from>237</Hsp_query-from>
> <Hsp_query-to>560</Hsp_query-to>
> <Hsp_hit-from>237</Hsp_hit-from>
> <Hsp_hit-to>560</Hsp_hit-to>
> <Hsp_query-frame>1</Hsp_query-frame>
> <Hsp_hit-frame>1</Hsp_hit-frame>
> <Hsp_identity>324</Hsp_identity>
> <Hsp_positive>324</Hsp_positive>
> <Hsp_align-len>324</Hsp_align-len>
>
> <Hsp_qseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACC
> TGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
> GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAA
> GCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCAC
> CTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGC
> CGAACGTATTTTTGCCGAACTTTT</Hsp_qseq>
>
> <Hsp_hseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACC
> TGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
> GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAA
> GCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCAC
> CTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGC
> CGAACGTATTTTTGCCGAACTTTT</Hsp_hseq>
>
> <Hsp_midline>|||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> |||||||||||||||||||||||||||</Hsp_midline>
> </Hsp>
>
> --------------------------------------------------------------
> ---------
>
> blastall -p blastn -m 0 -F T -d ecoli/ecoli.nt -i test.txt
>
> >gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section
> 1 of 400 of the
> >complete
> genome
> Length = 10596
>
> Score = 589 bits (297), Expect = e-168
> Identities = 315/324 (97%)
> Strand = Plus / Plus
>
>
> Query: 237
> aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 237
> aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296
>
>
> Query: 297
> cgggcnnnnnnnnncgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356
> |||||
> ||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 297
> cgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356
>
>
> Query: 357
> cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 357
> cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416
>
>
> Query: 417
> tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 417
> tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476
>
>
> Query: 477
> ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 477
> ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536
>
>
> Query: 537 cgaacgtatttttgccgaactttt 560
> ||||||||||||||||||||||||
> Sbjct: 537 cgaacgtatttttgccgaactttt 560
>
> --------------------------------------------------------------
> ---------
>
> blastall -p blastn -m 7 -F F -d ecoli/ecoli.nt -i test.txt
>
> <Hit>
> <Hit_num>1</Hit_num>
> <Hit_id>gi|1786181|gb|AE000111.1|AE000111</Hit_id>
> <Hit_def>Escherichia coli K-12 MG1655 section 1 of
> 400 of the
> complete genome</Hit_def>
> <Hit_accession>AE000111</Hit_accession>
> <Hit_len>10596</Hit_len>
> <Hit_hsps>
> <Hsp>
> <Hsp_num>1</Hsp_num>
> <Hsp_bit-score>1110.61</Hsp_bit-score>
> <Hsp_score>560</Hsp_score>
> <Hsp_evalue>0</Hsp_evalue>
> <Hsp_query-from>1</Hsp_query-from>
> <Hsp_query-to>560</Hsp_query-to>
> <Hsp_hit-from>1</Hsp_hit-from>
> <Hsp_hit-to>560</Hsp_hit-to>
> <Hsp_query-frame>1</Hsp_query-frame>
> <Hsp_hit-frame>1</Hsp_hit-frame>
> <Hsp_identity>560</Hsp_identity>
> <Hsp_positive>560</Hsp_positive>
> <Hsp_align-len>560</Hsp_align-len>
>
> <Hsp_qseq>AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAA
> AGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGA
> CTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGA
> GTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAG
> GTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
> CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTAC
> ATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGC
> AGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATG
> ATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTT
> TGCCGAACTTTT</Hsp_qseq>
>
> <Hsp_hseq>AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAA
> AGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGA
> CTTAGGTCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGA
> GTACACAACATCCATGAAACGCATTAGCACCACCATTACCACCACCATCACCATTACCACAG
> GTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGG
> CTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTAC
> ATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGC
> AGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATG
> ATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTT
> TGCCGAACTTTT</Hsp_hseq>
>
> <Hsp_midline>|||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> |||||||||||||||</Hsp_midline>
> </Hsp>
>
> --------------------------------------------------------------
> ---------
>
> blastall -p blastn -m 0 -F F -d ecoli/ecoli.nt -i test.txt
>
> >gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section
> 1 of 400 of the
> >complete
> genome
> Length = 10596
>
> Score = 1110 bits (560), Expect = 0.0
> Identities = 560/560 (100%)
> Strand = Plus / Plus
>
>
> Query: 1
> agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtc 60
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 1
> agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtc 60
>
>
> Query: 61
> tgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgacttagg 120
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 61
> tgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgacttagg 120
>
>
> Query: 121
> tcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagtac 180
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 121
> tcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagtac 180
>
>
> Query: 181
> acaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggt 240
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 181
> acaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggt 240
>
>
> Query: 241
> aacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcggg 300
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 241
> aacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcggg 300
>
>
> Query: 301
> ctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcggt 360
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 301
> ctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcggt 360
>
>
> Query: 361
> acatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgcc 420
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 361
> acatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgcc 420
>
>
> Query: 421
> aggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacctggtg 480
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 421
> aggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacctggtg 480
>
>
> Query: 481
> gcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgccgaa 540
>
> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
> Sbjct: 481
> gcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgccgaa 540
>
>
> Query: 541 cgtatttttgccgaactttt 560
> ||||||||||||||||||||
> Sbjct: 541 cgtatttttgccgaactttt 560
>
>
> >From: "Wiepert, Mathieu" <Wiepert.Mathieu at mayo.edu>
> >To: 'tai kwan do' <immunoguest at hotmail.com>, bioperl-l at bioperl.org
> >Subject: RE: [Bioperl-l] Difference between Date: Fri, 30
> Jan 2004 11:13:05
> >-0600
> >
> >Hi,
> >
> >I have a vague recollection of this problem, so this answer
> is likely
> >wrong, but I think it has something to do with the filtered
> sequence? You
> >have 9 masked NT's, so it is probably a difference in the
> defaults, and
> >something to do with the XML output not masked?
> >
> >Sorry I can't find the emails I had with NCBI on this, but I
> am maybe 70%
> >sure that it is a problem like that, with defaults on the
> local server
> >versus NCBI, and the XML not using masked data?
> >
> >Someone else chime in if I am way off there...
> >
> >HTH,
> >
> >-mat
> >
>
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