Difference between revisions of "Swiss-Prot"
From Christoph's Personal Wiki
(→Statistics) |
|||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
'''Swiss-Prot''' is a manually curated biological database of protein sequences started by Amos Bairoch and developed by the ''Swiss Institute of Bioinformatics'' and the ''European Bioinformatics Institute''.<ref name=Bairoch2000>Bairoch A (2000). "[http://bioinformatics.oupjournals.org/cgi/reprint/16/1/48 Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!]" ''Bioinformatics, 16:48-64</ref> | '''Swiss-Prot''' is a manually curated biological database of protein sequences started by Amos Bairoch and developed by the ''Swiss Institute of Bioinformatics'' and the ''European Bioinformatics Institute''.<ref name=Bairoch2000>Bairoch A (2000). "[http://bioinformatics.oupjournals.org/cgi/reprint/16/1/48 Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!]" ''Bioinformatics, 16:48-64</ref> | ||
| + | ==Content== | ||
Swiss-Prot strives to provide reliable protein sequences associated with a high level of annotation, including each of the following: *the description of the function of a protein; | Swiss-Prot strives to provide reliable protein sequences associated with a high level of annotation, including each of the following: *the description of the function of a protein; | ||
*its domains structure; | *its domains structure; | ||
| Line 9: | Line 10: | ||
*etc. | *etc. | ||
| − | Swiss-Prot and its automatically curated supplement TrEMBL, have joined with the ''Protein Information Resource'' protein database to produce the ''UniProt Knowledgebase'', the world's most comprehensive catalogue of information on proteins | + | ==Database types== |
| + | Swiss-Prot and its automatically curated supplement TrEMBL, have joined with the ''Protein Information Resource'' protein database to produce the ''UniProt Knowledgebase'', the world's most comprehensive catalogue of information on proteins. | ||
The UniProt consortium produced 3 database components, each optimised for different uses: | The UniProt consortium produced 3 database components, each optimised for different uses: | ||
*The UniProt Knowledgebase (UniProtKB (Swiss-Prot + TrEMBL)); | *The UniProt Knowledgebase (UniProtKB (Swiss-Prot + TrEMBL)); | ||
*The UniProt Non-redundant Reference (UniRef) databases, which combine closely related sequences into a single record to speed similarity searches; and | *The UniProt Non-redundant Reference (UniRef) databases, which combine closely related sequences into a single record to speed similarity searches; and | ||
| − | *The UniProt Archive (UniParc), which is a comprehensive repository of protein sequences, reflecting the history of all protein sequences. | + | *The UniProt Archive (UniParc), which is a comprehensive repository of protein sequences, reflecting the history of all protein sequences. |
| + | |||
| + | ==Statistics== | ||
| + | As of 11 July 2012, release "2012_07" of UniProtKB/Swiss-Prot contains 536,789 sequence entries (comprising 190,518,892 amino acids abstracted from 211,308 references) and release "2012_06" of UniProtKB/TrEMBL contains 226,60,469 sequence entries (comprising 7,407,531,063 amino acids).<ref name=SPstats>[http://www.expasy.org/sprot/relnotes/relstat.html UniProtKB/SwissProt release statistics]</ref><ref name=TrEMBLstats>[http://www.ebi.ac.uk/uniprot/TrEMBLstats/ UniProtKB/TrEMBL release statistics]</ref> | ||
| + | <!--As of 3 April 2007, UniProtKB/Swiss-Prot release 52.2 contains 263,525 entries. As of 3 April 2007, the UniProtKB/TrEMBL release 35.2 contains 4,232,122 entries.--> | ||
==References== | ==References== | ||
Latest revision as of 02:39, 13 July 2012
Swiss-Prot is a manually curated biological database of protein sequences started by Amos Bairoch and developed by the Swiss Institute of Bioinformatics and the European Bioinformatics Institute.[1]
Content
Swiss-Prot strives to provide reliable protein sequences associated with a high level of annotation, including each of the following: *the description of the function of a protein;
- its domains structure;
- post-translational modifications;
- variants;
- a minimal level of redundancy;
- a high level of integration with other databases;
- etc.
Database types
Swiss-Prot and its automatically curated supplement TrEMBL, have joined with the Protein Information Resource protein database to produce the UniProt Knowledgebase, the world's most comprehensive catalogue of information on proteins.
The UniProt consortium produced 3 database components, each optimised for different uses:
- The UniProt Knowledgebase (UniProtKB (Swiss-Prot + TrEMBL));
- The UniProt Non-redundant Reference (UniRef) databases, which combine closely related sequences into a single record to speed similarity searches; and
- The UniProt Archive (UniParc), which is a comprehensive repository of protein sequences, reflecting the history of all protein sequences.
Statistics
As of 11 July 2012, release "2012_07" of UniProtKB/Swiss-Prot contains 536,789 sequence entries (comprising 190,518,892 amino acids abstracted from 211,308 references) and release "2012_06" of UniProtKB/TrEMBL contains 226,60,469 sequence entries (comprising 7,407,531,063 amino acids).[2][3]
References
- ↑ Bairoch A (2000). "Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!" Bioinformatics, 16:48-64
- ↑ UniProtKB/SwissProt release statistics
- ↑ UniProtKB/TrEMBL release statistics
External links
- Swiss-Prot Protein Database (Swiss Institute of Bioinformatics)
- UniProt (Swiss Institute of Bioinformatics)
- Definition of Swiss-Prot format files
