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Nucleic Acids Research, 2003, Vol. 31, No. 13 3720-3722
© 2003 Oxford University Press

Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes

François Enault*, Karsten Suhre, Olivier Poirot, Chantal Abergel and Jean-Michel Claverie

Structural and Genomic Information (CNRS UPR2589), Institut de Biologie Structurale et Microbiologie, 31 chemin Joseph Aiguier, 13402 Marseille, cedex 20, France

*To whom correspondence should be addressed. Tel: +33 491164548; Fax: +33 491164549; Email: enault{at}igs.cnrs-mrs.fr

Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of ‘functionally interacting’ genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.


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