[Bioperl-l] Transcribe in bioperl

[Dan Kortschak]

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.