[Biopython] Back translation from Protein to RNA sequence

[Ivan Gregoretti]

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.

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.

Thank you,

Ivan






Ivan Gregoretti, PhD
Bioinformatics



On Mon, Apr 7, 2014 at 8:58 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> On Wed, Apr 2, 2014 at 5:33 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> > The documentation of the Seq object nicely shows how to
> >
> > 1) transcribe DNA -> RNA,
> > 2) back transcribe RNA -> DNA, and
> > 3) translate RNA -> protein.
> >
> > If priorities allow, I would appreciate the expansion of the documentation
> > with one example of
> >
> > 4) back translation protein -> most_probable_RNA.
> >
> > The result of that operation is species-dependent and worth documenting if
> > the functionality already exists.
> >
> > Thank you,
> >
> > Ivan
>
> Hello Ivan,
>
> Biopython currently deliberately does not have any
> back-translation functionality.
>
> Why do you want this, and how would you define it?
>
> I think 'most probable' would require a codon usage table
> for the organism, and would need a tie breaker for when
> two codons are equally frequent - or would you be happy
> with non-deterministic output?
>
> There are a whole set of details which would need to
> be settled, such as what would you do with ambiguous
> amino acids (e.g. X or J), making a general purpose
> back-translate rather complex.
>
> Last time this was discussed on the mailing list, the real
> use case was back-translation as used with protein to
> nucleotide alignment, where the sequence is known
> and just the gaps need inserting appropriately. e.g.
> https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
>
> Regards,
>
> Peter