Multiple Sequence Alignment

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Posted by Pradeep on January 29, 2005 at 04:33:43:

Hi,

I am writing code for MSA (multiple sequence alignment) as part of our 2nd semester project.

But I am facing difficulties in generating a PROFILE matrix for a group of aligned sequences and also implementing Linear Space Algorithm ( by Myers
and Miller) to profile- profile and sequence-profile alignment .

Could anyone please guide me in this matter also suggest the article for making profile matrix with gap opening and gap extension penalty column.

Waiting for your early reply ,

Regards
Pradeep.




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