[BioC] the diffrent alignment result between pairwiseAlignment() in Biostrings package and EBI-webserver

[Martin Morgan]

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_needle&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,
>


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