[Bioperl-l] PAML + Codeml problem

Neil Saunders n.saunders at uq.edu.au
Mon Aug 14 21:54:51 EDT 2006

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?

  School of Molecular and Microbial Sciences
  University of Queensland
  Brisbane 4072 Australia


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