Prolinks: a database of protein functional linkages derived from coevolution

Genome Biology
Volume 5
Issue 5

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Bowers PM
Pellegrini M
Thompson MJ
Fierro J
Yeates TO
Eisenberg D

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Bowers PM
Pellegrini M
Thompson MJ
Fierro J
Yeates TO
Eisenberg D
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Prolinks: a database of protein functional linkages derived from coevolution

Peter M Bowers¹, Matteo Pellegrini¹, Mike J Thompson¹, Joe Fierro², Todd O Yeates¹ and David Eisenberg¹

¹Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA

²454 Corporation, Branford, CT 06405, USA

author email corresponding author email

Genome Biology 2004, 5:R35


Published:	16 April 2004

Subject areas: Bioinformatics, Evolution, Microbiology and parasitology

Abstract

The advent of whole-genome sequencing has led to methods that infer protein function and linkages. We have combined four such algorithms (phylogenetic profile, Rosetta Stone, gene neighbor and gene cluster) in a single database - Prolinks - that spans 83 organisms and includes 10 million high-confidence links. The Proteome Navigator tool allows users to browse predicted linkage networks interactively, providing accompanying annotation from public databases. The Prolinks database and the Proteome Navigator tool are available for use online at http://dip.doe-mbi.ucla.edu/pronav webcite.