[Bioperl-l] compare sequences codon by codon

[Jason Stajich]

wow - my incomplete typing was amazing...  trying again :->

To identify identical codons easiest is probably just walk back  
through the alignment columns in sets of 3.  Have a look at the  
pairwise_kaks script and the HOWTO at http://bioperl.org/wiki/ 
HOWTO:PAML. These shows bits and pieces which may be of interest. The  
key routine is aa_to_dna_aln in the Bio::Align::Utilities module.

On Feb 18, 2009, at 8:36 AM, Jason Stajich 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,
>> manni122.
>> -- 
>> View this message in context: http://www.nabble.com/compare-sequences-codon-by-codon-tp22081753p22081753.html
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
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>
> Jason Stajich
> jason at bioperl.org
>
>
>

Jason Stajich
jason at bioperl.org