[Bioperl-l] Transcribe in bioperl

Jason Stajich jason at bioperl.org
Mon Jan 25 16:26:55 EST 2010


It was already implemented several years ago -- reverse_translate  
Bio::Tools::CodonTable -> revtanslate


   my $seqobj    = Bio::PrimarySeq->new(-seq => 'FHGERHEL');
   my $iupac_str = $myCodonTable->reverse_translate_all($seqobj);


Chris had meant to say reverse_transcribe of RNA -> DNA FWIW.

-jason
On Jan 25, 2010, at 1:24 PM, Peter wrote:

> On Mon, Jan 25, 2010 at 9:00 PM, Dan Kortschak
> <dan.kortschak at adelaide.edu.au> wrote:
>> A reverse_translate to IUPAC degenerate codes is not a bad idea,
>> particularly for PCR primer design.
>
> 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.
>
> We debated this back and forth for Biopython, and decided to leave it
> out. It wasn't possible for a simple back translate to a simple  
> string to
> handle the use cases we considered, and other options like returning
> a regular expression covering all possible back translations were too
> complex (for a core sequence method/function).
>
> Peter
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
http://twitter.com/hyphaltip



More information about the Bioperl-l mailing list