[Bioperl-l] PAML + Codeml problem..

[Chris Fields]

Brian,

Would having a custom codon table work?  Since TGA->'U' requires a nearby
SECIS element, theoretically a gene could have one 'TGA' codon that codes
for 'U' (nearby SECIS element) and another 'TGA' codon that codes for the
actual stop (no SECIS element).

I don't think there is a way to have position-specific TGA->U based on
user-input either (a flag, perhaps).  That's the only work-around for it I
can think of.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Brian Osborne
> Sent: Monday, August 14, 2006 4:49 PM
> To: Xianjun Dong
> Cc: bioperl-l at lists.open-bio.org; aaron.j.mackey at gsk.com;
> golharam at umdnj.edu
> Subject: Re: [Bioperl-l] PAML + Codeml problem..
> 
> 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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> 
> 
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