Hi Zongfu, I'm still looking into this but wanted to give you an update since you have been waiting. I believe these differences in output occur when multiple pairwise alignments produce the maximum alignment score. In this case a decision must be made about which alignment to report. As explained on the man page, pairwiseAlignment() reports the alignment with the smallest initial deletion whose mismatches occur before its insertions and deletions. p <- "AGTA" s <- "ACCTA" > pairwiseAlignment(p, s, type="global") Global PairwiseAlignedFixedSubject (1 of 1) pattern: [1] AG-TA subject: [1] ACCTA score: -13.95402 The 'G' could align to either 'C' but the alignment reported has the 'G' before the insertion/deletion. This is consistent with the rules stated on the pairwiseAlignment() man page. The same situation occurs with the "ND" in your example below. You may want to contact EBI support to ask how they choose to report an alignment when more than one give the max score. I'm not sure it's realistic to expect a perfect match between the output of EBI and pairwiseAlignment(). The EBI interface for the global algorithm has additional parameters that pairwiseAlignment() does not and I'm not sure how these are used. The global-local and local-global options in pairwiseAlignment() are not the same as the straight global and local and are not, as far as I can see, offered through the EBI interface. Valerie On 12/29/2011 08:46 PM, Valerie Obenchain wrote: > On 12/28/11 20:36, cao zongfu wrote: >> Anyone can help me?Thanks. >> >> Zongfu > > Hi Zongfu, > > Martin is out of the office for the holidays. I'm looking at this and > hope to have an answer for you soon. > > Valerie >> >> >> ---------- Forwarded message ---------- >> From: cao zongfu<caozongfu at="" gmail.com=""> >> Date: 2011/12/24 >> Subject: Re: [BioC] the diffrent alignment result between >> pairwiseAlignment() in Biostrings package and EBI-webserver >> To: Martin Morgan<mtmorgan at="" fhcrc.org=""> >> >> >> Hi, Martin, >> For exmple, >> >> require("Biostrings") >> data(BLOSUM62) >> x1 = >> "QVQLVQSGAEVKKPGSSVKVSCKTSGDTFSTYAISWVRQAPGQGLEWMGGIIPIFGKAHYAQKFQG RVTITADESTSTAYMELSSLRSEDTAVYFCARKFHFVSGSPFGMDVWGQGTTVTVSS" >> >> x2 = >> "QVQLVESGGDVVQPGGSLRLSCAASGVAFSNYGMHWVRQAPGKGLEWVAVIWYDGSNKYYADSVKG RFTISRDNSKNMLYLQMNSLRAEDTAMYYCARNDDYWGQGTLVTVSS" >> >> >> alm<- pairwiseAlignment(x1, x2, substitutionMatrix=BLOSUM62, gapOpening= >> -10, gapExtension= -0.5,type="global-local") >> alm >> >> pattern: [1] >> QVQLVQSGAEVKKPGSSVKVSCKTSGDTFSTYAISWVRQAPGQGLEWMGGIIPIFGKAHYAQKFQGR VTITADESTSTAYMELSSLRSEDTAVYFCARKFHFVSGSPFGMDVWGQGTTVTVSS >> >> subject: [1] >> QVQLVESGGDVVQPGGSLRLSCAASGVAFSNYGMHWVRQAPGKGLEWVAVIWYDGSNKYYADSVKGR FTISRDNSKNMLYLQMNSLRAEDTAMYYCAR >> >> ND----------DYWGQGTLVTVSS >> >> And the result from EBI webserver are as follows >> x1 1 QVQLVQSGAEVKKPGSSVKVSCKTSGDTFSTYAISWVRQAPGQGLEWMGG 50 >> x2 1 QVQLVESGGDVVQPGGSLRLSCAASGVAFSNYGMHWVRQAPGKGLEWVAV 50 >> >> x1 51 IIPIFGKAHYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYFCARKF 100 >> x2 51 IWYDGSNKYYADSVKGRFTISRDNSKNMLYLQMNSLRAEDTAMYYCAR-- 98 >> >> x1 101 HFVSGSPFGMDVWGQGTTVTVSS 123 >> x2 99 --------NDDYWGQGTLVTVSS 113 >> >> >> we can find, the position of "ND" are different in the two alignment >> result. one is before the gap, and the other after the gap. >> Thanks, >> >> Zongfu >> >> >> >> >> >> >> 2011/12/24 Martin Morgan<mtmorgan at="" fhcrc.org=""> >>> On 12/22/2011 11:54 PM, cao zongfu wrote: >>>> Dear Prof., Hi >>>> I have compared the results of pairwise alignment from >>>> pairwiseAlignment() in Biostrings package and the webserver of >>>> >> http://www.ebi.ac.uk/Tools/services/web/toolform.ebi?tool=emboss_ne edle&context=protein >> >> , >>>> I found the results are different. >>>> >>>> EBI-web parameters are as follows, >>>> #matrix=BLOSUM62 >>>> #GAP OPEN=10 >>>> #GAP EXTEND=0.5 >>>> #OUTPUT FORMAT="PAIR" >>>> #END GAP PENALTY=FALSE >>>> #END GAP OPEN=10 >>>> #END GAP EXTEND=0.5 >>>> and the parameters in pairwiseAlignment() are as follows, >>>> alm<- pairwiseAlignment(x1, x2, substitutionMatrix=BLOSUM62, >>>> gapOpening= >>>> -10, gapExtension= -0.5,type="global-local") >>>> >>>> I have tried to set the type="global", they all wored well, but the >>>> alignment result is still different.I want to know how to set other >>>> parameters in order to get the identical alignment result as EBI >> webserver? >>> >>> can you provide a more explicit example, with sequences x1 and x2 as >>> well >> as the output from the two programs? Martin >>>> Thanks, >>>> >>> >>> -- >>> Computational Biology >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >>> >>> Location: M1-B861 >>> Telephone: 206 667-2793 >> >> >> >> -- >> >> Zongfu Cao >> >> BeiGene(Beijing) Co.,Ltd >> No.30 Science Park Road >> Zhong-Guan-Cun Life Science Park >> Changping District, Beijing P.R.China >> Postal Code: 102206 >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor