[Bioperl-l] PAML + Codeml problem..

Chris Fields cjfields at uiuc.edu
Mon Aug 14 16:26:37 EDT 2006

You are correct, sir! (sorry, bad Ed McMahon impression)

I don't know of any translation program that recognizes TGA as
selenocysteine as you would have to run a concurrent search for a SECIS
element using RNA motif software. 

Most of the time when I have seen 'U' present for a protein it is added
either b/c:

1) there is biochemical evidence to support the presence of selenocysteine, 
2) the protein is homologous to one that is known to have 'U' (most common),

3) or the protein suspected to have one based on prior searches for SECIS
elements using various RNA motif search programs
(http://en.wikipedia.org/wiki/SECIS_element).  RNAMotif comes to mind,


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of aaron.j.mackey at gsk.com
> Sent: Monday, August 14, 2006 2:11 PM
> To: Brian Osborne
> Cc: bioperl-l at lists.open-bio.org; Xianjun Dong; golharam at umdnj.edu
> Subject: Re: [Bioperl-l] PAML + Codeml problem..
> > > 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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