[Bioperl-l] Transcribe in bioperl

Aaron Mackey ajmackey at gmail.com
Tue Jan 26 08:24:43 EST 2010


There's also Bio::Tools::IUPAC; given a sequence with IUPAC ambiguity codes,
it provides a SeqIO stream that enumerates all the possible unambiguous
realizations.  Not the right solution for every situation, but quite useful
when you need it.

-Aaron


On Mon, Jan 25, 2010 at 4:38 PM, Dan Kortschak <
dan.kortschak at adelaide.edu.au> wrote:

> 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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