[Biojava-l] Ambiguity codes.

[Eric Blossom]

Shouldn't this be a problem only for importers (parsers) and exporters of
data? Shouldn't data models in biojava be able to define amino acids and
nucleic acids including ambiguous ones independent of alphabet?

Eric Blossom              mailto:Eric@BlossomAssociates.Com
Blossom Associates West   http://www.BlossomAssociates.Com/
                          510 841-3338

On Wed, 21 Jun 2000, David Martin wrote:

> > 
> > 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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