UniProt release 10.0

Published March 6, 2007

Headlines

UniProtKB/Swiss-Prot major release (52.0)

UniProt Knowledgebase release 10.0 includes Swiss-Prot release 52.0 and TrEMBL release 35.0.

UniProtKB/Swiss-Prot release 52.0 of March 6, 2007 contains 260'175 sequence entries, comprising 95'002'661 amino acids abstracted from 152'564 references. 18'986 sequences have been added since release 51.0: this represents an increase of 7.3%. In addition, the annotations of 190'910 entries have been revised.

Many improvements were carried out in the last 4 months:

We have reintroduced the initiator methionine: the UniProtKB sequence data now always corresponds to the precursor form of a protein, i.e. before post-translational modifications such as cleavage of the signal peptide or other events (except of course when the sequence data are derived from direct protein sequencing).
We have extended the UniProtKB accession number format: we have extended the existing accession number format by allowing the first character to be any of the 26 letters (instead of only O, P and Q).
We have added cross-references to 7 new databases and introduced a new molecule type for the EMBL cross-references (Viral_cRNA)

UniProtKB/Swiss-Prot (flat file version) turned 1 Gigabyte (GB) long on this major release ! For comparison, the human genome contains 0.791175 GB of data (the 3.1647 x 10^9 base pairs represented as 2-bits)

UniProtKB News

Format change in the dbxref.txt document file

The dbxref.txt file lists the names and abbreviations and URLs of all databases cross-referenced in the UniProt Knowledgebase. We have added a new optional field, "Ref". This field contains the database reference in the following format:

Ref   : Journal_abbrev Volume:First_page-Last_page(YYYY); [PubMed=Pubmed_identifier; ][DOI=Digital_object_identifier;]

Example:

     Abbrev: PROSITE
     Name  : PROSITE; a protein domain and family database
     Ref   : Nucleic Acids Res. 34:D227-D230(2006); PubMed=16381852; DOI=10.1093/nar/gkj063;
     LinkTp: Explicit
     Server: http://www.expasy.org/prosite/
     Db_URL: www.expasy.org/cgi-bin/get-prosite-raw.pl?%s
     Cat   : Family and domain databases

Changes concerning keywords

New keyword:

Kallmann syndrome