[Bioperl-l] Transcribe in bioperl

Dan Kortschak dan.kortschak at adelaide.edu.au
Mon Jan 25 16:38:44 EST 2010


Good to see that these ideas have been considered.

I'd be interested to see this discussion, or at least the point dealing
with the problems that might arise. I'm at a loss as to how ambiguity
codes can't completely describe all possible coding sequences for any
given codon table (via Bio::Tools::CodonTable - in fact this already has
the revtranslate that could be fitted into a Bio::PrimarySeq method - to
answer Mark and Jason's comments, I think that /if/ a reverse_translate
method exists, it makes logical sense to have it tied to a sequence
object, calling the B:T:CT method on the seq object itself rather than
only in Bio::Tools, 2¢). Pete, tcn you provide an example of the
problems?

thanks
Dan

On Mon, 2010-01-25 at 21:24 +0000, Peter wrote:
> I would say it could be a bad idea. For any protein string there are
> multiple possible back translations, and this cannot be captured
> fully as a nucleotide string even using the IUPAC ambiguity chars.




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