[Biopython] Back translation support in Biopython

[Igor Rodrigues da Costa]

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