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

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

Research output: Contribution to journalArticle

12 Citations (Scopus)

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/.

Original languageEnglish
Pages (from-to)3720-3722
Number of pages3
JournalNucleic Acids Research
Volume31
Issue number13
DOIs
Publication statusPublished - 1 Jul 2003
Externally publishedYes

Fingerprint

Bacterial Genomes
Bacterial Genes
Proteins
Escherichia coli
Genes
Bacterial Proteins
Escherichia coli Proteins
Open Reading Frames
Genome

ASJC Scopus subject areas

  • Genetics

Cite this

Phydbac (phylogenomic display of bacterial genes) : An interactive resource for the annotation of bacterial genomes. / Enault, François; Suhre, Karsten; Poirot, Olivier; Abergel, Chantal; Claverie, Jean Michel.

In: Nucleic Acids Research, Vol. 31, No. 13, 01.07.2003, p. 3720-3722.

Research output: Contribution to journalArticle

Enault, François ; Suhre, Karsten ; Poirot, Olivier ; Abergel, Chantal ; Claverie, Jean Michel. / Phydbac (phylogenomic display of bacterial genes) : An interactive resource for the annotation of bacterial genomes. In: Nucleic Acids Research. 2003 ; Vol. 31, No. 13. pp. 3720-3722.
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