title: PairsDB atlas of protein sequence space.
abstract: Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually on each request, results are retrieved instantaneously from a database of pre-computed alignments. Filtering options allow you to find a set of sequences satisfying a set of criteria-for example, all human proteins with solved structure and without transmembrane segments. PairsDB is continually updated and covers all sequences in Uniprot. The data is stored in a MySQL relational database. Data files will be made available for download at ftp://nic.funet.fi/pub/sci/molbio. PairsDB can also be accessed interactively at http://pairsdb.csc.fi. PairsDB data is a valuable platform to build various downstream automated analysis pipelines. For example, the graph of all-against-all similarity relationships is the starting point for clustering protein families, delineating domains, improving alignment accuracy by consistency measures, and defining orthologous genes. Moreover, query-anchored stacked sequence alignments, profiles and consensus sequences are useful in studies of sequence conservation patterns for clues about possible functional sites.
authors.affiliation: MRC Functional Genetics Unit, University of Oxford, UK.
authors.forename: Andreas
authors.initials: A
authors.lastname: Heger
authors.forename: Eija
authors.initials: E
authors.lastname: Korpelainen
authors.forename: Taavi
authors.initials: T
authors.lastname: Hupponen
authors.forename: Kimmo
authors.initials: K
authors.lastname: Mattila
authors.forename: Vesa
authors.initials: V
authors.lastname: Ollikainen
authors.forename: Liisa
authors.initials: L
authors.lastname: Holm
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface