[Bioperl-l] PAML + Codeml problem..

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Mon Aug 14 15:11:21 EDT 2006


> > 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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