[Bioperl-l] PAML + Codeml problem..

Brian Osborne osborne1 at optonline.net
Mon Aug 14 14:55:35 EDT 2006


Xianjun,

You're going to have to answer these questions yourself by examining
CodonTable.pm and then selecting the appropriate table.

Brian O.


On 8/14/06 11:57 AM, "Xianjun Dong" <xianjun.dong at bccs.uib.no> wrote:

> But I still have some questions:
> 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?




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