[Bioperl-l] PAML + Codeml problem

aaron.j.mackey at gsk.com aaron.j.mackey at gsk.com
Tue Aug 15 09:42:38 EDT 2006

> > 'J' is an odd one; haven't seen that one used before.  Is there a 
> > 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:


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.


More information about the Bioperl-l mailing list