[Bioperl-l] compare sequences codon by codon

Jason Stajich jason at bioperl.org
Wed Feb 18 11:36:15 EST 2009

Have you tried any of the code on aligning sequences at the protein  
level - mapping back to codons.  To identify identical codons easiest  
is probably just walk back through the alignment columns in sets of.  
the pairwise_kaks script and the http://bioperl.org/wiki/HOWTO:PAML  
shows bits and pieces of this - the key routines is aa_to_dna_aln in  
the Bio::Align::Utilities module.

Show us some code and I'm sure we can help better.

On Feb 18, 2009, at 7:55 AM, manni122 wrote:

> Hi there, I hope one of you can help me...
> I am looking for a way to compare two DNA sequences codon by codon  
> that have
> been previously pairwise aligned. So I want to have the information  
> on which
> codon position the pair is identical and on which not.
> Is there something like this implemented in Bioperl?
> Thanks for every help,
> manni122.
> -- 
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Jason Stajich
jason at bioperl.org

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