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

[Fernan Aguero]

+----[ Peter Rice <pmr at ebi.ac.uk> (04.Jun.2007 13:18):
|
| 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? 

4.0.0 from the Rocks Bio Roll (x86_64).

| 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,

Thanks for the prompt reply. Are the changes to antigenic
(at least some) already in CVS? 

Fernan