Phydbac "gene function predictor"

A gene annotation tool based on genomic context analysis

François Enault, Karsten Suhre, Jean Michael Claverie

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

Background: 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. Results: 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%. Conclusion: 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 http://www.igs.cnrsmrs.fr/phydbac/indexPS.html.

Original languageEnglish
Article number247
JournalBMC Bioinformatics
Volume6
DOIs
Publication statusPublished - 12 Oct 2005
Externally publishedYes

Fingerprint

Molecular Sequence Annotation
Genomics
Annotation
Predictors
Genes
Gene
Protein
Genome
Proteins
Databases
Prediction
Web Server
Metabolic Networks and Pathways
Gene encoding
Linkage
Escherichia Coli
Pairwise
Pathway
High Accuracy
Encoding

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Phydbac "gene function predictor" : A gene annotation tool based on genomic context analysis. / Enault, François; Suhre, Karsten; Claverie, Jean Michael.

In: BMC Bioinformatics, Vol. 6, 247, 12.10.2005.

Research output: Contribution to journalArticle

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