PairsDB atlas of protein sequence space

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.

• Publication year

  2007

• Venue

  Nucleic Acids Res.

• Publication date

  2007-11-05

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/gkm879PMID 17986464PMCID 2238971
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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