[bip] Swiss-Flash bulletin of 18-Jan-2008

[Bruce Southey]

Hi,
Sorry if you already know about this, but I am forwarding this because
I think it is sufficiently important for people know about it. See the
note regarding ClustalW.

Regards
Bruce

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* Swiss-Flash bulletin of 18-Jan-2008 *
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Swiss-Flash reports news of databases, software and service developments
from the groups at the Swiss Institute of Bioinformatics that are
responsible for the ENZYME, PROSITE, SWISS-2DPAGE, Swiss-Prot and
TrEMBL databases; the Melanie software package; the ExPASy WWW server
the SWISS-MODEL, Swiss-Shop and other network-based computational tools;
the Core Facilities services.

To subscribe or unsubscribe to Swiss-Flash, connect to the following URL:
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In this Swiss-Flash bulletin:

UniProt: Important format change in protein sequence lines
	By Elisabeth Gasteiger

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UniProt
Important format change in protein sequence lines
By Elisabeth Gasteiger (Elisabeth.Gasteiger at isb-sib.ch)

Forthcoming changes to the UniProtKB format are announced at
     http://www.expasy.org/sprot/relnotes/sp_soon.html .
This document is updated continuously, and we do not regularly send
out announcements of forthcoming changes by email.

However, as one of the planned format changes is very likely to affect
many existing tools and programs, we want to mention it explicitly:
We will modify the UniProtKB sequence lines to use the IUPAC/IUBMB
recommended one-letter codes 'U' for selenocysteine and 'O' for pyrrolysine.
We will also introduce a new feature key 'NON_STD' to represent these
non-standard amino acids.
This change will take effect with UniProt release 13.0 of 26-Feb-2008.

We therefore strongly recommend that you look at
     http://www.expasy.org/sprot/relnotes/sp_soon.html#FT_NON_STD

if you are maintaing any software dealing with UniProt sequence lines.

Note: We have noticed that current versions of ClustalW do not handle
      pyrrolysine (O) correctly: Amino acids 'O' are deleted from the
      sequences in the alignment. We were told that this will be fixed
      in the next version.




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