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Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis

François Enault*, Karsten Suhre and Jean-Michel Claverie

Author Affiliations

Structural and Genomic Information, CNRS – UPR 2589, 31 chemin Joseph Aiguier, 13009 Marseille, France

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BMC Bioinformatics 2005, 6:247  doi:10.1186/1471-2105-6-247

Published: 12 October 2005



The large amount of completely sequenced genomes allows genomic context analysis to predict reliable functional associations between prokaryotic proteins. Major methods rely on the fact that genes encoding physically interacting partners or members of shared metabolic pathways tend to be proximate on the genome, to evolve in a correlated manner and to be fused as a single sequence in another organism.


The new "Gene Function Predictor", linked to the web server Phydbac proposes putative associations between Escherichia coli K-12 proteins derived from a combination of these methods. We show that associations made by this tool are more accurate than linkages found in the other established databases. Predicted assignments to GO categories, based on pre-existing functional annotations of associated proteins are also available. This new database currently holds 9,379 pairwise links at an expected success rate of at least 80%, the 6,466 functional predictions to GO terms derived from these links having a level of accuracy higher than 70%.


The "Gene Function Predictor" is an automatic tool that aims to help biologists by providing them hypothetical functional predictions out of genomic context characteristics. The "Gene Function predictor" is available at webcite.