[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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