[Bioperl-l] PAML + Codeml problem

Chris Fields cjfields at uiuc.edu
Tue Aug 15 00:48:18 EDT 2006


...And pyrrolysine is 'Pyl' (found it on the web).  Wonder what they'll use
when more naturally occurring amino acids are found! Maybe they'll do what
NOAA does for hurricanes and revert to the Greek alphabet. ; >

I'll go ahead and add these to Bio::SeqUtils.  We'll beat the GenBank
incorporation date!

Chris

> -----Original Message-----
> From: Neil Saunders [mailto:n.saunders at uq.edu.au]
> Sent: Monday, August 14, 2006 11:31 PM
> To: Chris Fields
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] PAML + Codeml problem
> 
> Chris Fields wrote:
> > 'J' is an odd one; haven't seen that one used before.  Is there a valid
> > three-letter code for that?
> 
> It was new to me too.  Apparently it's used where I/L are
> indistinguishable in
> mass spectrometry.  The 3-letter code is Xle.  As of October 2006, GenBank
> are
> making it legal:
> 
> http://www.bio.net/bionet/mm/genbankb/2006-June/000241.html
> 
> Neil
> --
>   School of Molecular and Microbial Sciences
>   University of Queensland
>   Brisbane 4072 Australia
> 
> http://nsaunders.wordpress.com



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