[Bioperl-l] PAML + Codeml problem

Chris Fields cjfields at uiuc.edu
Tue Aug 15 00:21:38 EDT 2006


In a previous post, Brian indicated that Bio::Tools::CodonTable inherits
codon tables from Bio::SeqUtils, which includes selenocysteine.  It does not
include 'J' or 'O', but the other ambiguous codes are all present. 

'J' is an odd one; haven't seen that one used before.  Is there a valid
three-letter code for that?


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Neil Saunders
> Sent: Monday, August 14, 2006 8:55 PM
> To: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] PAML + Codeml problem
> Not a solution to the original post, but I thought it worth pointing out
> that as
> IUPAC have now adopted "O" for amino acid 22, pyrrolysine, any
> alphabetical
> character is now valid in a protein sequence:
> B=D/N, J=I/L, O=pyrrolysine, U=selenocysteine, X=unknown, Z=E/Q
> Leaving aside issues like how other software deals with this and how
> databases
> deal with translated stop codons (or not), I just wondered if any BioPerl
> modules require changes to reflect this?
> Neil
> --
>   School of Molecular and Microbial Sciences
>   University of Queensland
>   Brisbane 4072 Australia
> http://nsaunders.wordpress.com
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