Hi Simon, EMBOSS 6.0.1 no longer replaces pyrrolysine with a gap (neither did a fully patched 5.0.0 AFAIR). Thanks to Isabelle for the memory jog/hint.
Alan > Our regular update of uniprot threw up some warnings when we updated > over the weekend. It's not clear from the error which line in the entry > is problematic, but it doesn't seem to have caused any major problems > and I can still retrieve and query the sequences from the indices > created. > > We're still on EMBOSS v4 (I know I should update - but it works for what > we use it for!). Is this something which is fixed in later versions or > is it something new in uniprot itself? > > I'll paste in a couple of the 174 warnings I got. > > Cheers > > Simon. > > [formatdb] WARNING: Sequence number 176991 (lcl|MTBB1_METBF), 1 illegal > character was removed: > 1 - > > [formatdb] WARNING: Sequence number 176992 (lcl|MTBB1_METMA), 1 illegal > character was removed: > 1 - > > [formatdb] WARNING: Sequence number 176993 (lcl|MTBB2_METAC), 1 illegal > character was removed: > 1 - > > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
