[Bioperl-l] compare sequences codon by codon

[Mark A. Jensen]

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 
>> 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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>>> 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
>
>
>
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