[Biopython] Back translation from Protein to RNA sequence

[Peter Cock]

On Mon, Apr 7, 2014 at 3:20 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> Hello Peter,
>
> I would benefit from the availability of a back-translation tool for
> practical reasons.
>
> In our case, part of my team is designing peptides. They asked my if I
> had a python tool to create the corresponding DNA so that they could
> design and order expression vectors.
>
> As simple as that. I would not intend to use this tool out of context
> and I fully understand that a codon bias table would be necessary for
> each species.

OK, so in your case you specifically want non-ambiguous codons
(just using A, C, G, T and not trying to capture the wobble codon or
other many-to-one mapping possibilities with IUPAC codes like N),
and when picking each codon you'd probably like this to be based
on tRNA levels on your target organism to maximise efficiency.

It should be simple to write a special case function for your needs
with a dictionary mapping each amino acid to a preferred codon
(for each target organism).

> I just leave it then as an open question then in case somebody has
> written a programme within the scope or our need. I'll explore the
> pico_galaxy link you sent me nonetheless.

It wouldn't be relevant to your use-case.

Peter