TY - JOUR
T1 - The SUPERFAMILY database in 2007
T2 - Families and functions
AU - Wilson, Derek
AU - Madera, Martin
AU - Vogel, Christine
AU - Chothia, Cyrus
AU - Gough, Julian
N1 - Funding Information:
We gratefully acknowledge comments on the manuscript from Madan Babu Mohan. C. V. acknowledges support by the Boehringer Ingelheim Fonds, the Medical Research Council and the International Human Frontier of Science Program. Funding to pay the Open Access publication charges for this article was provided by the Medical Research Council.
PY - 2007/1
Y1 - 2007/1
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkl910
DO - 10.1093/nar/gkl910
M3 - Article
C2 - 17098927
AN - SCOPUS:33846044585
SN - 0305-1048
VL - 35
SP - D308-D313
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -