Nucleic Acids Research Advance Access originally published online on November 26, 2008
Nucleic Acids Research 2009 37(Database issue):D380-D386; doi:10.1093/nar/gkn762
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Nucleic Acids Research, 2009, Vol. 37, Database issue D380-D386
© 2008 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.
This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]
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SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny
1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, 2Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK and 3Institute for Cellular and Molecular Biology University of Texas at Austin 2500 Speedway, MBB 3.210 Austin, TX 78712 USA
*To whom correspondence should be addressed. Tel: +44 1223 402479; Fax: +44 1223 213556; Email: dw{at}mrc-1mb.cam.ac.uk
Received September 15, 2008. Revised October 5, 2008. Accepted October 6, 2008.
SUPERFAMILY provides structural, functional and evolutionary information for proteins from all completely sequenced genomes, and large sequence collections such as UniProt. Protein domain assignments for over 900 genomes are included in the database, which can be accessed at http://supfam.org/. Hidden Markov models based on Structural Classification of Proteins (SCOP) domain definitions at the superfamily level are used to provide structural annotation. We recently produced a new model library based on SCOP 1.73. Family level assignments are also available. From the web site users can submit sequences for SCOP domain classification; search for keywords such as superfamilies, families, organism names, models and sequence identifiers; find over- and underrepresented families or superfamilies within a genome relative to other genomes or groups of genomes; compare domain architectures across selections of genomes and finally build multiple sequence alignments between Protein Data Bank (PDB), genomic and custom sequences. Recent extensions to the database include InterPro abstracts and Gene Ontology terms for superfamiles, taxonomic visualization of the distribution of families across the tree of life, searches for functionally similar domain architectures and phylogenetic trees. The database, models and associated scripts are available for download from the ftp site.
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