[EMBOSS] antigenic + valid ambiguity (aa residue) codes (BUG?)

[Peter Rice]

Fernan Aguero wrote:
> we're running antigenic on a number of sequences
> which contain some ambiguous residues. 
> 
> It seems like antigenic doesn't like the '*', 'B', 'U', 'Z' and
> 'X' characters in protein sequences.

Which version of EMBOSS are you running? O is now a valid amino acid character. 
In earlier releases it was treated as a phylip gap character.

The algorithm in antigenic uses a published table that only has values for the 
20 naturally occurring amino acids.

We can add average values for ambiguity codes (weighted). We have no data for U 
and O, but we can convert them to X.

In the next release, antigenic will accept any protein sequence.

regards,

Peter Rice