+----[ Peter Rice <[EMAIL PROTECTED]> (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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
