title: Annotation of bacterial genomes using improved phylogenomic profiles.
abstract: BACKGROUND
  Phylogenomic profiling is a large-scale comparative genomic method used to infer protein function from evolutionary information first described in a binary form by Pellegrini et al. (1999). Here, we propose improvements of this approach including the use of normalized Blastp bit scores, a normalization of the matrix of profiles to take into account the evolutionary distances between bacteria, the definition of a phylogenomic neighborhood based on continuous pairwise distances between genes and an original annotation procedure including the computation of a p-value for each functional assignment.
  
  
  RESULTS
  The method presented here increases the number of Ecocyc enzymes identified as being evolutionarily related by about 25% with respect to the original binary form (absent/present) method. The fraction of 'false' positives is shown to be smaller than 20%. Based on their phylogenomic relationships, genes of unknown function can then be automatically related to annotated genes. Each gene annotation predicted is associated with a p-value, i.e. its probability to be obtained by chance. The validity of this method was extensively tested on a large set of genes of known function using the MultiFun database. We find that 50% of 3122 function attributions that can be made at a p-value level of 10(-11) correspond to the actual gene annotation. The method can be readily applied to any newly sequenced microbial genome. In contrast to earlier work on the same topic, our approach avoids the use of arbitrary cut-off values, and provides a reliability estimate of the functional predictions in form of p-values.
authors.affiliation: Structural and Genomic Information, CNRS-UPR 2589, 31 chemin Joseph Aiguier, 13009 Marseille, France. enault@igs.cnrs-mrs.fr
authors.forename: F
authors.initials: F
authors.lastname: Enault
authors.forename: K
authors.initials: K
authors.lastname: Suhre
authors.forename: C
authors.initials: C
authors.lastname: Abergel
authors.forename: O
authors.initials: O
authors.lastname: Poirot
authors.forename: J-M
authors.initials: JM
authors.lastname: Claverie
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D004282:Documentation; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D010802:Phylogeny; D020543:Proteome / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D020543:Proteome