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_needl e&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? Thanks, -- 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 [[alternative HTML version deleted]]

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_nee dle&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