SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

By Derek Wilson, Ralph Pethica, Yiduo Zhou, Charles Talbot, Christine Vogel, Martin Madera, Cyrus Chothia, Julian Gough. 2008

474 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

The SWISS-MODEL Repository—new features and functionality (2016, background): “The computational structural biology community has a long tradition of providing protein model databases such as the Genomic Threading Database (4,5), ModBase (6), Genome 3D (7), GPCRdb (8) and SWISS-MODEL Repository (SMR) (9) as well as protein functional annotation databases such as Superfamily (1”
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures (2013, methodology): “Other methods such as SUPERFAMILY (9,10) and SCOPmap (11) have been developed to automatically classify new PDB structures in the context of SCOP and have the advantage of operating on proteins somewhat dissimilar from those already classified.”
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses (2012, unknown): “html Wilson et al. (2009)”
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line (2010, background): “The human genome encodes, for example, B600 RNA-binding proteins (Wilson et al, 2009) many of which may have regulatory functions.”
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria (2013, methodology): “All studied TFs were classified into 55 protein families based on their domain composition in the Pfam [36], COG [37] and Superfamily [38] libraries (see TF families classification and domains architecture in Additional file 1).”
Consensus protein design (2016, methodology): “The most efficient way to acquire sequences is via sequence alignment databases such as Pfam (Sonnhammer et al., 1998; Finn et al., 2016), Prosite (Sigrist et al., 2013), SMART (Letunic et al., 2015) and Superfamily (Wilson et al., 2009).”
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis (2011, methodology): “tool for evolutionary analyses (35), while superfamily phylogenetic profiling has proven to be an effective tool in identifying functionally linked proteins (36).”