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?

Thanks,

-- 

Zongfu Cao

*BeiGene(Beijing) Co.,Ltd*
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Changping District, Beijing P.R.China
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