[EMBOSS] Illegal character warnings in uniprot

[Wells, Isabelle]

Hi,
These errors are due to the non standard amino acid pyrrolysine O. I've
been getting them for a couple months. I am not sure whether this was
fixed in the later versions of EMBOSS, we are still on v4 as well.
Best regards,
Isabelle

-----Original Message-----
From: emboss-bounces at lists.open-bio.org
[mailto:emboss-bounces at lists.open-bio.org] On Behalf Of simon andrews
(BI)
Sent: Monday, September 08, 2008 09:35
To: emboss at emboss.open-bio.org
Subject: [EMBOSS] Illegal character warnings in uniprot

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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