[Bioperl-l] Translate sequences align and reverse translate

Jason Stajich jason at bioperl.org
Thu Jan 18 12:50:54 EST 2007


bp_pairwise_kaks does most of this for you (you can use clustalw and  
muscle).

  at the core is aa_to_dna_align() routine from Bio::Align::Utilities


-jason
On Jan 18, 2007, at 5:44 AM, Anthony Underwood wrote:

> Hi All,
>
>
>
> I would like to automate the process of taking coding DNA sequences,
> translating them to amino acids, aligning them with clustalw and then
> reverse-translating back to DNA so as to obtain the best alignment. I
> can think of how I would do this with bioperl but since it is  
> probably a
> common process  I would like to ask if anyone already has such a  
> script
> that they wouldn't mind sharing so I don't re-invent the wheel.
>
>
>
> Many thanks,
>
>
>
> Anthony
>
>
>
>
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--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html




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