PairsDB atlas of protein sequence space.

Journal article

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: Heger, A; Korpelainen, E; Hupponen, T; Mattila, K; Ollikainen, V

• Publication status: Published
• Journal: Nucleic acids research
• Volume: 36
• Issue: Database issue
• Pages: D276-D280
• Publication date: 2008-01-01
• DOI: 10.1093/nar/gkm879
• EISSN: 1362-4962
• ISSN: 0305-1048
• Language: English
• Keywords: Humans; Databases, Protein; Amino Acid Sequence; User-Computer Interface; Conserved Sequence; Internet; Sequence Alignment; Sequence Analysis, Protein