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.
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https://hal.inria.fr/hal-00746864
Contributor : Marie-France Sagot <>
Submitted on : Monday, October 29, 2012 - 6:56:29 PM
Last modification on : Thursday, March 21, 2019 - 2:51:28 PM

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Yves-Pol Deniélou, Marie-France Sagot, Frédéric Boyer, Alain Viari. Bacterial syntenies: an exact approach with gene quorum.. BMC Bioinformatics, BioMed Central, 2011, 12, pp.193. ⟨10.1186/1471-2105-12-193⟩. ⟨hal-00746864⟩

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