[Bioperl-l] PAML + Codeml problem

[aaron.j.mackey at gsk.com]

> > '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

for the curios, the appearance of J was first noted in IUPAC nomenclature 
committees in 1999:

 
http://www.blackwell-synergy.com/doi/pdf/10.1046/j.1432-1327.1999.news99.x

and had to do with ambiguous NMR (not mass-spec) signals (which is why 
Selenocysteine was awarded the U instead of the J).

But yes, regardless of why I and L can't be distinguished, J is the 
ambiguity code for the pair.

-Aaron