title: SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.
abstract: 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.
authors.affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK. dw@mrc-1mb.cam.ac.uk
authors.forename: Derek
authors.initials: D
authors.lastname: Wilson
authors.forename: Ralph
authors.initials: R
authors.lastname: Pethica
authors.forename: Yiduo
authors.initials: Y
authors.lastname: Zhou
authors.forename: Charles
authors.initials: C
authors.lastname: Talbot
authors.forename: Christine
authors.initials: C
authors.lastname: Vogel
authors.forename: Martin
authors.initials: M
authors.lastname: Madera
authors.forename: Cyrus
authors.initials: C
authors.lastname: Chothia
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
mesh_terms: D000818:Animals; D003196:Computer Graphics; D030562:Databases, Protein; D023281:Genomics; D006801:Humans; D010802:Phylogeny; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins