[Bioperl-l] compare sequences codon by codon
markus.liebscher at gmx.de
Wed Feb 18 11:52:51 EST 2009
thanks for this suggestion. I will read through and hopefully present some
best wishes, manni122
Jason Stajich-3 wrote:
> 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,
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> Jason Stajich
> jason at bioperl.org
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