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

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 o...

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Veröffentlicht in:BMC bioinformatics Jg. 6; H. 1; S. 247
Hauptverfasser: Enault, François, Suhre, Karsten, Claverie, Jean-Michel
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England BioMed Central 12.10.2005
BMC
Schlagworte:
Algorithms
Benchmarking
Chromosome Mapping - methods
Databases, Protein
Escherichia coli
Escherichia coli K12 - genetics
Escherichia coli Proteins - genetics
Gene Fusion
Internet
Life Sciences
Models, Genetic
Multigene Family
Phylogeny
Quantitative Methods
Sequence Alignment
Sequence Homology, Amino Acid
Software
Phylogenetic Profile
Acyl Carrier Protein
Putative Association
Pairwise Association
Intergenic Distance
ISSN:1471-2105, 1471-2105
Online-Zugang:Volltext
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Zusammenfassung: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 http://www.igs.cnrs-mrs.fr/phydbac/indexPS.html.
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-6-247