[Bioperl-l] Difference between
Jason Stajich
jason at cgt.duhs.duke.edu
Tue Feb 3 10:45:55 EST 2004
One also gets slightly different values at times in -m 8 and -m 0 runs as well.
-jason
On Tue, 3 Feb 2004, Wiepert, Mathieu wrote:
> 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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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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