[Biojava-l] Ambiguity codes.

[David Martin]

> 
> I've been here before Matt. 
> 
> It sucks. Not least in-real-life N in DNA can mean "don't match me" or
> "i'm a gap between contigs" or "i'm a base with no knowledge of the base"

Hmm.. Do we have to do all of those? I have always used N,X = any base and
.=not any base. 

WU-BLAST have jsut decided that -= indeterminate length of nothing which
at least makes some sort of sense.

N,X anything
. one nothing
- many nothings

fun it is..

I cheated and said 'thats horrible. Give me nice data instead'

..d
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