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help with written algorithm - modification

stranistranic
New User

May 3, 2016, 3:59 AM

Post #1 of 3 (2163 views)

help with written algorithm - modification	Can't Post

Hi,

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

http://www.perlmonks.org/?node_id=819506

how I modify that program write also max score?

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

Laurent_R
Veteran / Moderator

May 8, 2016, 10:12 AM

Post #2 of 3 (2127 views)

Re: [stranistranic] help with written algorithm - modification [In reply to]	Can't Post

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

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

stranistranic
New User

May 8, 2016, 11:24 AM

Post #3 of 3 (2123 views)

Re: [Laurent_R] help with written algorithm - modification [In reply to]	Can't Post

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/

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