[Bioperl-l] PAML + Codeml problem..

[Brian Osborne]

Xianjun,

I spoke too soon. I'd assumed that NCBI had a table to handle
selenocysteine, but it does not:

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c

These tables are the basis for the Bio::Tools::CodonTable module, and the
CodonTable module looks to be up-to-date with respect to NCBI's page. You
can solve your problem by making a custom table using the add_table()
method, see t/CodonTable.t for a nice example. Your custom table will look
something like the Euplotid Nuclear Code table, which translates TGA to C.
You should be able to translate TGA to U since the amino acid codes that
CodonTable inherits from Bio::SeqUtils contain "U" and "Sec".

This is an issue that's independent of the issue raised by Aaron, I'm
assuming you know whether or not your sequences should be translated this
way.

Brian O.


On 8/14/06 3:11 PM, "aaron.j.mackey at gsk.com" <aaron.j.mackey at gsk.com> wrote:

>>> 1. For the case which in-frame stop codon codes for
> selenocysteine('U'),
>>> like the transcript ENSMUST00000094469, it should be translated into
>>> 'U', not '*' since the IUPAC/IUBMB has officially recommended it. But
>>> when I use the codontable_id=1(generic codon table), it still was '*'.
>>> Is it because the package(Bio::Tools::CodonTable) is not so updated as
>>> the IUPAC rules?
> 
> The translation of TGA into Selenocysteine (U) is not "universal", it only
> occurs when the downstream UTR contains a SECIS RNA element;
> Bio::Tools::CodonTable is unable to differentiate such
> selenocysteine-encoding TGA codons from "normal" TGA stop codons,
> regardless of the translation table in use.  GenBank/EMBL-formatted
> records will typically have /transl_except entries in the feature table,
> but the BioPerl "translate" method does not (yet) recognize these (someone
> correct me if I'm wrong).
> 
> -Aaron
> 
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