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help with written algorithm - modification

New User

May 3, 2016, 3:59 AM

Views: 2306
help with written algorithm - modification


I have found algorithm on perlmonk for sequence alignment, algorithm work fine:


how I modify that program write also max score?

(This post was edited by stranistranic on May 3, 2016, 4:00 AM)

Veteran / Moderator

May 8, 2016, 10:12 AM

Views: 2270
Re: [stranistranic] help with written algorithm - modification

You have to explain what exactly you mean by max score.

Most people here are not biologists and have trouble understanding these things.

New User

May 8, 2016, 11:24 AM

Views: 2266
Re: [Laurent_R] help with written algorithm - modification

sorry, the max score is in the matrix where you go throught named traceback step. The best alignment amoung the alignments can be identified using the maxsimum alignment score from match, mismatch and gap, which may be user defined.

I hope I help you.

the same is in the smith waterman algorithmhttp://etutorials.org/Misc/blast/Part+II+Theory/Chapter+3.+Sequence+Alignment/3.2+Local+Alignment+Smith-Waterman/