[Bioperl-l] compare sequences codon by codon
Mark A. Jensen
maj at fortinbras.us
Wed Feb 18 12:41:35 EST 2009
Ah! Sets of 3!
----- Original Message -----
From: "Jason Stajich" <jason at bioperl.org>
To: "manni122 Liebscher" <markus.liebscher at gmx.de>
Cc: "bioperl list" <Bioperl-l at lists.open-bio.org>
Sent: Wednesday, February 18, 2009 12:26 PM
Subject: Re: [Bioperl-l] compare sequences codon by codon
> 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
>> 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
>>> been previously pairwise aligned. So I want to have the information on
>>> codon position the pair is identical and on which not.
>>> Is there something like this implemented in Bioperl?
>>> Thanks for every help,
>>> View this message in context:
>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>> Jason Stajich
>> jason at bioperl.org
> Jason Stajich
> jason at bioperl.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l