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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
