[Bioperl-l] Translate sequences align and reverse translate

Roy Chaudhuri roy at colibase.bham.ac.uk
Thu Jan 18 14:25:47 UTC 2007

> 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.

align_on_codons.pl in the examples/align directory looks like it does 
what you want (I've never used it, though).

Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.


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