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Does it exist the module for Smith Waterman algoritm?



stranistranic
New User

Apr 29, 2016, 12:25 AM


Views: 9816
Does it exist the module for Smith Waterman algoritm?

Hi,

I need existing module for local alignment - Smith Waterman algoritm. Such as for global alignment - Needleman Wunsch i use Algorithm::NeedlemanWunsch.

Does it exist S-W? I found just MILLER_MYERS... I need already done version for comparison.

I hope you can help me.Tnx


Laurent_R
Veteran / Moderator

Apr 29, 2016, 9:53 AM


Views: 9810
Re: [stranistranic] Does it exist the module for Smith Waterman algoritm?

Hmm, no idea if this is what you are looking for, but take a look at:
http://search.cpan.org/dist/BioPerl/Bio/Tools/pSW.pm
and
http://search.cpan.org/~cjfields/BioPerl-1.6.924/Bio/Tools/dpAlign.pm
and:
http://search.cpan.org/dist/BioPerl/Bio/Search/HSP/FastaHSP.pm

Also take a look at this:
https://www.google.fr/search?q=cpan+Smith+Waterman&ie=utf-8&oe=utf-8&gws_rd=cr&ei=ZZAjV4LEPMrWU5mwv1A