[Bioperl-l] How to pull a codon by position from a rich sequence object

Phillip San Miguel pmiguel at purdue.edu
Wed Apr 14 16:08:49 EDT 2010

I have a list of mutations positions (snps) in a reference genome 
(yeast). I would like to know what amino acid substitutions, if any, 
these mutations cause. How best to do this?

So my dream method would be called from a rich sequence object and take 
a single position (absolute base position in the genome) as an  argument 
and return the 3 base codon containing this position and an index (1, 2, 
or 3) of which base of the codon the argument was. Then I could 
translate the original codon and the mutant codon to get my answer using 
the Bio::Tools::CodonTable object.

Any such bioperl method? Any other recommendations? This would be fairly 
simple, were there not multiple exons to consider.


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