[Biojava-l] Alphabet Manager

[Matthew Pocock]

Hi.

Neither Thomas nor I are protein people. I have no problem with the more 
esoteric amino-acids being added, either directly or to an extended 
alphabet. One way to get arround this is to add U as an ambiguity symbol 
that matches just one amino-acid (whatever it is a modified form of - 
I'm showing my lack of knowledge now). This way, it becomes an alias for 
compute reasons (like DP), but is still identifiable. I'ts a bit of a 
hack, but it will work out fine. Methylated DNA bases could be handled 
with the same trick - methylated ambiguities for each base.

Roll on 1.2!

Matthew

Emig, Robin wrote:

> 	Maybe we should include that in an ExtendedAminoAcids Alphabet?
> -Robin
> 
> -----Original Message-----
> From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]On
> Behalf Of Cox, Greg
> Sent: Thursday, February 15, 2001 1:26 PM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Alphabet Manager
> 
> 
> Are there any objections to including 'U' (selenocysteine) to the amino
> acids alphabet?  This can wait until after 1.1 if people want.
> 
> Greg
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