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. 2007 Jan;35(Database issue):D308-13.
doi: 10.1093/nar/gkl910. Epub 2006 Nov 10.

The SUPERFAMILY database in 2007: families and functions

Derek Wilson  1 , Martin Madera, Christine Vogel, Cyrus Chothia, Julian Gough
Affiliations

The SUPERFAMILY database in 2007: families and functions

Derek Wilson et al. Nucleic Acids Res. 2007 Jan.

Abstract

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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Figures

Figure 1
Figure 1
Summary of the functionality and results that are available as part of the SUPERFAMILY analysis framework via the web interface.
Figure 2
Figure 2
Domain architecture and assignment details for the Ensembl protein ENSP00000315147 from human. Shown are the superfamily and family classification and associated E-values for two domains. Links to further family details, alignments between the SUPERFAMILY model and the protein, assignments for the human genome and domain combinations in which the superfamily domain occur in are included for each domain.
See this image and copyright information in PMC

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