[Bioperl-l] Transcribe in bioperl

Peter biopython at maubp.freeserve.co.uk
Mon Jan 25 16:24:33 EST 2010


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


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