Prolinks: a database of protein functional linkages derived from coevolution.
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.
Bowers
Peter M
PM
Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
Pellegrini
Matteo
M
Thompson
Mike J
MJ
Fierro
Joe
J
Yeates
Todd O
TO
Eisenberg
David
D
D025181:ATP Synthetase Complexes / Q000235:genetics; D000818:Animals; D019843:Archaeal Proteins / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D019985:Benchmarking / Q000379:methods; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D002633:Chemotaxis / Q000502:physiology; D000075202:Contraindications; D030562:Databases, Protein; D029721:Drosophila Proteins / Q000502:physiology; D019143:Evolution, Molecular; D008040:Genetic Linkage / Q000235:genetics*; D008070:Lipopolysaccharides / Q000096:biosynthesis; D010802:Phylogeny; D011506:Proteins / Q000502:physiology*; D040901:Proteomics / Q000379:methods; D029701:Saccharomyces cerevisiae Proteins / Q000502:physiology
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D008070:Lipopolysaccharides; D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins; D025181:ATP Synthetase Complexes