[EMBOSS] Illegal character warnings in uniprot

[simon andrews (BI)]

OK thanks.  Guess I've found an excuse to upgrade at last...

Cheers

Simon. 

> -----Original Message-----
> From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk] 
> Sent: 08 September 2008 11:18
> To: simon andrews (BI)
> Cc: emboss at emboss.open-bio.org
> Subject: Re: [EMBOSS] Illegal character warnings in uniprot
> 
> 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 -
> >
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> >
> 
> 
>