title: Bacterial syntenies: an exact approach with gene quorum.
abstract: BACKGROUND
  The automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems.
  
  
  RESULTS
  In this paper, we present a versatile tool to extract all syntenies from multiple bacterial species based on a clear-cut and very flexible definition of the synteny blocks that allows for gene quorum, partial gene correspondence, gaps, and a partial or total conservation of the gene order.
  
  
  CONCLUSIONS
  We apply this tool to two different kinds of studies. The first one is a search for functional gene associations. In this context, we compare our tool to a widely used heuristic--I-ADHORE--and show that at least up to ten genomes, the problem remains tractable with our exact definition and algorithm. The second application is linked to evolutionary studies: we verify in a multiple alignment setting that pairs of orthologs in synteny are more conserved than pairs outside, thus extending a previous pairwise study. We then show that this observation is in fact a function of the size of the synteny: the larger the block of synteny is, the more conserved the genes are.
authors: INRIA Grenoble-Rhône-Alpes, Team BAMBOO, 655 Avenue de l'Europe, 38334 Montbonnot Cedex, France. yves-pol.denielou@laposte.net
authors: Yves-Pol
authors: YP
authors: Deniélou
authors: Marie-France
authors: MF
authors: Sagot
authors: Frédéric
authors: F
authors: Boyer
authors: Alain
authors: A
authors: Viari
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