[EMBOSS] Illegal character warnings in uniprot

[ajb at ebi.ac.uk]

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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