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The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver.

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Peer-reviewed

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Article

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Authors

Pandurangan, Arun Prasad 
Stahlhacke, Jonathan 
Oates, Matt E 
Smithers, Ben 
Gough, Julian 

Abstract

Here, we present a major update to the SUPERFAMILY database and the webserver. We describe the addition of new SUPERFAMILY 2.0 profile HMM library containing a total of 27 623 HMMs. The database now includes Superfamily domain annotations for millions of protein sequences taken from the Universal Protein Recourse Knowledgebase (UniProtKB) and the National Center for Biotechnology Information (NCBI). This addition constitutes about 51 and 45 million distinct protein sequences obtained from UniProtKB and NCBI respectively. Currently, the database contains annotations for 63 244 and 102 151 complete genomes taken from UniProtKB and NCBI respectively. The current sequence collection and genome update is the biggest so far in the history of SUPERFAMILY updates. In order to the deal with the massive wealth of information, here we introduce a new SUPERFAMILY 2.0 webserver (http://supfam.org). Currently, the webserver mainly focuses on the search, retrieval and display of Superfamily annotation for the entire sequence and genome collection in the database.

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Keywords

Databases, Protein, Genome, Internet, Markov Chains, Protein Domains, Proteome, Sequence Analysis, Protein

Journal Title

Nucleic Acids Res

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Journal ISSN

0305-1048
1362-4962

Volume Title

47

Publisher

Oxford University Press (OUP)