Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2008 Jan;36(Database issue):D276-80.
doi: 10.1093/nar/gkm879. Epub 2007 Nov 5.

PairsDB atlas of protein sequence space

Andreas Heger  1 , Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, Liisa Holm
Affiliations

PairsDB atlas of protein sequence space

Andreas Heger et al. Nucleic Acids Res. 2008 Jan.

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.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
(a) Data storage model and (b) Functionality of the PairsDB web server.
See this image and copyright information in PMC

References

    1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Promponas VJ, Enright AJ, Tsoka S, Kreil D, Leroy C, Hamodrakas S, Sander C, Ouzounis CA. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics. 2000;16:915–922. - PubMed
    1. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 2001;305:567–580. - PubMed
    1. Lupas A, van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science. 1991;252:1162–1164. - PubMed
    1. Heger A, Holm L. Exhaustive enumeration of protein domain families. J. Mol. Biol. 2003;328:749–767. - PubMed

Publication types