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Nucleic Acids Research Advance Access originally published online on November 5, 2007
Nucleic Acids Research 2008 36(Database issue):D276-D280; doi:10.1093/nar/gkm879
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Nucleic Acids Research, 2008, Vol. 36, Database issue D276-D280
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

PairsDB atlas of protein sequence space

Andreas Heger1,2, Eija Korpelainen3, Taavi Hupponen3, Kimmo Mattila3, Vesa Ollikainen3 and Liisa Holm2,4,*

1MRC Functional Genetics Unit, University of Oxford, UK, 2Institute of Biotechnology, University of Helsinki, 3Center for Scientific Computing (CSC), Espoo and 4Department of Biological and Environmental Sciences, Division of Genetics, University of Helsinki, Finland

*To whom correspondence should be addressed. Tel: +358 9 19159115; Fax: +358 9 19159079; Email: liisa.holm{at}helsinki.fi

Received August 17, 2007. Revised September 28, 2007. Accepted October 1, 2007.

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.


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