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Nucleic Acids Research Advance Access published online on November 10, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl910
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

The SUPERFAMILY database in 2007: families and functions

Derek Wilson*, Martin Madera1, Christine Vogel2, Cyrus Chothia and Julian Gough3

MRC Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH, UK 1 Biomolecular Engineering, University of California Santa Cruz Santa Cruz, CA 95064, USA 2 Institute for Cellular and Molecular Biology, University of Texas at Austin Austin, TX, USA 3 Unite de Bioinformatique Structurale, Institute Pasteur 25-28 Rue du Docteur Roux 75724 Paris Cedex, Paris, France

*To whom correspondence should be addressed. Tel: +44 1223 402479; Fax: +44 1223 213556; Email: superfamily{at}mrc-lmb.cam.ac.uk

Received September 15, 2006. Revised October 11, 2006. Accepted October 12, 2006.

The SUPERFAMILY database provides protein domain assignments, at the SCOP ‘superfamily’ level, for the predicted protein sequences in over 400 completed genomes. A superfamily groups together domains of different families which have a common evolutionary ancestor based on structural, functional and sequence data. SUPERFAMILY domain assignments are generated using an expert curated set of profile hidden Markov models. All models and structural assignments are available for browsing and download from http://supfam.org. The web interface includes services such as domain architectures and alignment details for all protein assignments, searchable domain combinations, domain occurrence network visualization, detection of over- or under-represented superfamilies for a given genome by comparison with other genomes, assignment of manually submitted sequences and keyword searches. In this update we describe the SUPERFAMILY database and outline two major developments: (i) incorporation of family level assignments and (ii) a superfamily-level functional annotation. The SUPERFAMILY database can be used for general protein evolution and superfamily-specific studies, genomic annotation, and structural genomics target suggestion and assessment.


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