Swiss-Prot release 43 available

Elisabeth Gasteiger Elisabeth.Gasteiger at isb-sib.ch
Wed Apr 7 02:36:20 EST 2004


(I) DATABASE AVAILABILITY ANNOUNCEMENT


Name        : Swiss-Prot
Description : Protein knowledgebase.
Release     : 43.0 of March 2004
Statistics  : 146'720 fully annotated sequences, 54'093'154 amino acids,
               113'719 references.
Citations   : Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C.,
               Estreicher A., Gasteiger E., Martin M.J., Michoud K.,
               O'Donovan C., Phan I., Pilbout S. and Schneider M.
               The Swiss-Prot protein knowledgebase and its supplement
               TrEMBL in 2003.
               Nucleic Acids Res. 31:365-370(2003).

               Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B.,
               Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M.,
               Martin M.J., Natale D.A., O'Donovan C., Redaschi N. and
               Yeh L.S.
               UniProt: the Universal Protein knowledgebase.
               Nucleic Acids Res. 32:D115-D119(2004).

Availability: FTP: ftp://ftp.expasy.org/databases/uniprot/knowledgebase
                    ftp://ftp.expasy.org/databases/swiss-prot
                    ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase
                    ftp://ftp.ebi.ac.uk/pub/databases/swissprot
               WWW: http://www.expasy.org/sprot/
                    http://www.ebi.ac.uk/sprot/


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(II) SUMMARY OF CURRENT CHANGES AND FUTURE DEVELOPMENTS IN SWISS-PROT.

Note: a much more complete description of the changes and future developments
is available from the release notes. The release notes can be accessed from the
WWW at the address:

              http://www.expasy.org/sprot/relnotes/

or downloaded by FTP from:

      ftp://ftp.expasy.org/databases/swiss-prot/release/relnotes.htm
      ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release/relnotes.htm


A) Summary of the changes in Swiss-Prot release 43

In Swiss-Prot:

- Release 43.0 of Swiss-Prot contains 146'720 sequence entries, comprising
   54'093'154 amino acids abstracted from 113'719 references.
   10'760 sequences have been added since release 42, the sequence data of
   663 existing entries has been updated and the annotations of
   44'948 entries have been revised. This represents an increase of 8%.

- The High-quality Automated and Manual Annotation of microbial Proteomes
   (HAMAP) project is progressing. It aims to annotate a significant
   percentage of proteins which originate from microbial genome sequencing
   projects. There are currently 167 complete proteomes in Swiss-Prot and
   TrEMBL. The HAMAP web site was enhanced with many new features:

       http://www.expasy.org/sprot/hamap/

- The Human Proteomics Initiative (HPI) project is progressing. There are
   currently 10'691 annotated human sequences in Swiss-Prot. Up-to-date
   detailed statistics concerning the HPI project, as well as detailed
   project information, are available at:

       http://www.expasy.org/sprot/hpi/

- A new comment (CC) topic 'RNA EDITING' has been introduced to convey
   information relevant to all types of RNA editing that lead to one or more
   amino acid changes.

- We have added cross-references from Swiss-Prot to the following databases:
   DictyBase, PhotoList and RGD. Links to DictyDB have been removed
   in agreement with the maintainers of both DictyDB and DictyBase.

- All the recent changes to Swiss-Prot format are described in detail
   in the continuously updated document:

       http://www.expasy.org/sprot/relnotes/sp_news.html

- The ExPASy WWW server was the target of many improvements that are all
   described at the address: http://www.expasy.org/history.html


B) Future developments

Forthcoming format changes are listed in the continuously updated document
http://www.expasy.org/sprot/relnotes/sp_soon.html


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Swiss-Prot is copyright.  It is produced through a collaboration between the
Swiss Institute  of  Bioinformatics   and the EMBL Outstation - the European
Bioinformatics Institute. There are no restrictions on its use by non-profit
institutions as long as its  content is in no way modified. Usage by and for
commercial entities requires a license agreement.  For information about the
licensing  scheme  see: http://www.isb-sib.ch/announce/ or send  an email to
license at isb-sib.ch.
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Elisabeth Gasteiger
Swiss Institute of Bioinformatics
CMU - 1, rue Michel Servet                Tel. (+41 22) 379 58 75
CH - 1211 Geneva 4 Switzerland            Fax  (+41 22) 379 58 58
Elisabeth.Gasteiger at isb-sib.ch            http://www.expasy.org/
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