The SUPERFAMILY database in 2007: families and functions

被引：175

作者：

Wilson, Derek

Madera, Martin

Vogel, Christine

Chothia, Cyrus

Gough, Julian

机构：

[1] MRC, Mol Biol Lab, Cambridge CB2 2QH, England

[2] Univ Calif Santa Cruz, Santa Cruz, CA 95064 USA

[3] Univ Texas, Inst Cellular & Mol Biol, Austin, TX 78712 USA

[4] Inst Pasteur, Unite Bioinformat Struct, F-75724 Paris, France

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

基金：

英国医学研究理事会;

关键词：

D O I：

10.1093/nar/gkl910

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D308 / D313

页数：6

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