[BioPython] Translation issues

[Peter]

On 1/28/08, Renato Alves <rjalves at igc.gulbenkian.pt> wrote:
> Hi.
>
> I'm trying to automate and validate the process of translation in
> sequences downloaded from NCBI.  ...  The problem is
> that the starting aminoacid in NCBI is always M but with the Translation
> module isn't, even if the codon is marked as "starting" in the
> corresponding codon table.
>
> So, is this the right behavior or am I missing something?

Sadly, that is the just way the translation module works.  This is a
fairly common problem, and its one I was planning to try and "fix" as
part of Bug 2382
http://bugzilla.open-bio.org/show_bug.cgi?id=2381

I would like some comments on the ideas on that bug - for example
would you prefer separate methods/functions for blind translation,
translation until a stop codon, and translation from a start codon
which is treated as an M - or a single method with lots of optional
arguments?

> Any other suggestions to do this test will also help.

Right now, I would check the start codon yourself and then use an M
when translating the sequence.  Remember the codon table (table 11 in
your example) should have all the valid start codons defined.

Peter