[Bioperl-l] Alignment optimization using degenerate code

Dave Messina David.Messina at sbc.su.se
Sun Feb 8 11:24:11 EST 2009

Pairwise alignment algorithms, when run with typical parameters, typically
minimize gaps anyway.

I'm puzzled by your idea of changing the codons. If you're aligning DNA, you
can't just change the sequence to improve the alignment.

This sounds like a homework problem. I suggest you read up on the basics of
pairwise sequence alignment algorithms and maybe even try doing the
alignments by hand. That should lead to an understanding of how gaps are


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