[Biopython] Back translation support in Biopython

[Eric Talevich]

Hi Igor,

It sounds like you're referring to aligning amino acid sequences to codon
sequences, as PAL2NAL does. This is different from what most people mean by
back translation, but as you point out, certainly useful.

If you write a function that can match a protein sequence alignment to a
set of raw CDS sequences, returning a nucleotide alignment based on the
codon-to-amino-acid mapping, that would be useful. However, PAL2NAL does
exactly that, plus a bit more, and is a fairly well-known and easily
obtained program. Personally, I would prefer to write a wrapper for PAL2NAL
under Bio.Align.Applications, using the existing Bio.Applications framework.

Once the user has a codon alignment, dn/ds and many other calculations
based on evolutionary models can be performed with our PAML wrappers, under
Bio.Phylo.PAML. I agree there is room in Biopython to make this workflow
easier to perform. (Although I wouldn't be able to mentor such a project
under GSoC this year.)

Best,
Eric


On Tue, Apr 3, 2012 at 5:24 PM, Igor Rodrigues da Costa <
igorrcosta at hotmail.com> wrote:

>
> Thanks for your response!
> I think back translation has an obvious solution that avoids all those
> problems mentioned in that discussion you cited, that is to pass the
> nucleotide sequence as a parameter. It has plenty of utilities, I have used
> it in my own research for comparing the evolutionary profile (ks/ka) of a
> list of aligned proteins in a multifasta (I made a script that fetched the
> CDS from ncbi using Entrez module to get the nucleotide sequence), it
> aligns the codons of nucleotide sequences (a hard problem if the protein
> sequence is not available) and can also check for data integrity.
> Another topic of interest, also used in my projects, is the calculation of
> the Dn/Ds rate (non-synonymous / synonymous mutations * non-synonymous /
> synonymous loci) using the most popular models (Nei-Gojobori, Li, etc). It
> is very usefull as can be seen for it's widespread use in papers (
> http://code.google.com/p/kaks-calculator/wiki/Citations)
> Similar projects:
> https://github.com/tanghaibao/bio-pipeline/tree/master/synonymous_calculation/
> http://www.bork.embl.de/pal2nal/
> http://cran.r-project.org/web/packages/seqinr/index.html
> http://services.cbu.uib.no/tools/kaks
> http://code.google.com/p/kaks-calculator/
> Thanks for your input,Igor
> > Date: Sun, 1 Apr 2012 09:51:12 +0100
> > Subject: Re: [Biopython] Back translation support in Biopython
> > From: p.j.a.cock at googlemail.com
> > To: igorrcosta at hotmail.com
> > CC: biopython at lists.open-bio.org
> >
> > On Sun, Apr 1, 2012 at 4:04 AM, Igor Rodrigues da Costa
> > <igorrcosta at hotmail.com> wrote:
> > >
> > > Hi,
> > > I am interested in participating in GSoC this summer. I would
> > > like to know if there is community support for a new project:
> > > Extending Seq class to add support to back translation of
> > > proteins (something like this: http://www.bork.embl.de/pal2nal/ ).
> > > If this project isn't strong enough at its own, it could be added
> > > to any existing project, or it could be complemented with others
> > > suggestions from the community.
> > > Thanks for your attention,Igor
> >
> > Hi Igor,
> >
> > I don't think back translation in itself is nearly enough to be a
> > GSoC project. Is it also problematic - we had a good long
> > discussion about back translation, and what it might be useful
> > for, back in 2008. In particular, assuming back translation to
> > a simple nucleotide sequence (as a string or Seq object),
> > what would it actually be useful for?
> >
> > See http://bugzilla.open-bio.org/show_bug.cgi?id=2618 which
> > is now using https://redmine.open-bio.org/issues/2618 and
> > the quite long and at times confusing thread:
> > http://lists.open-bio.org/pipermail/biopython/2008-October/004588.html
> >
> > Did you have any other ideas or topics that interested you?
> >
> > Regards,
> >
> > Peter
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>