title: Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes.
abstract: 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/.
authors.affiliation: Structural and Genomic Information (CNRS UPR2589), Institut de Biologie Structurale et Microbiologie, 31 chemin Joseph Aiguier, 13402 Marseille, cedex 20, France. enault@igs.cnrs-mrs.fr
authors.forename: François
authors.initials: F
authors.lastname: Enault
authors.forename: Karsten
authors.initials: K
authors.lastname: Suhre
authors.forename: Olivier
authors.initials: O
authors.lastname: Poirot
authors.forename: Chantal
authors.initials: C
authors.lastname: Abergel
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Claverie
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000145:classification* / Q000235:genetics / Q000502:physiology; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D020407:Internet; D016366:Open Reading Frames; D010802:Phylogeny; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins