Phydbac2

Improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis

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

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Phydbac (phylogenomic display of bacterial genes) implemented a method of phylogenomic profiling using a distance measure based on normalized BLAST scores. This method was able to increase the predictive power of phylogenomic profiling by about 25% when compared to the classical approach based on Hamming distances. Here we present a major-extension of Phydbac (named here Phydbac2), that extends both the concept and the functionality of the original web-service. While phylogenomic profiles remain the central focus of Phydbac2, it now integrates chromosomal proximity and gene fusion analyses as two additional non-similarity-based indicators for inferring pairwise gene functional relationships. Moreover, all presently available (January 2004) fully sequenced bacterial genomes and those of three lower eukaryotes are now included in the profiling process, thus increasing the initial number of reference genomes (71 in Phydbac) to 150 in Phydbac2. Using the KEGG metabolic pathway database as a benchmark, we show that the predictive power of Phydbac2 is improved by 27% over the previous version. This gain is accounted for on one hand, by the increased number of reference genomes (11%) and on the other hand, as a result of including chromosomal proximity into the distance measure (16%). The expanded functionality of Phydbac2 now allows the user to query more than 50 different genomes, including at least one member of each major bacterial group, most major pathogens and potential bio-terrorism agents. The search for co-evolving genes based on consensus profiles from multiple organisms, the display of Phydbac2 profiles side by side with COG information, the inclusion of KEGG metabolic pathway maps the production of chromosomal proximity maps, and the possibility of collecting and processing results from different Phydbac queries in a common shopping cart are the main new features of Phydbac2. The Phydbac2 web server is available at http://igsserver.cnrs-mrs.fr/phydbac/.

Original languageEnglish
JournalNucleic Acids Research
Volume32
Issue numberWEB SERVER ISS.
DOIs
Publication statusPublished - 1 Jul 2004
Externally publishedYes

Fingerprint

Bacterial Genes
Genome
Metabolic Networks and Pathways
Genes
Terrorism
Bacterial Genomes
Benchmarking
Gene Fusion
Eukaryota
Databases

ASJC Scopus subject areas

  • Genetics

Cite this

Phydbac2 : Improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. / Enault, François; Suhre, Karsten; Poirot, Olivier; Abergel, Chantal; Claverie, Jean Michel.

In: Nucleic Acids Research, Vol. 32, No. WEB SERVER ISS., 01.07.2004.

Research output: Contribution to journalArticle

Enault, François ; Suhre, Karsten ; Poirot, Olivier ; Abergel, Chantal ; Claverie, Jean Michel. / Phydbac2 : Improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. In: Nucleic Acids Research. 2004 ; Vol. 32, No. WEB SERVER ISS.
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