Bacterial syntenies: an exact approach with gene quorum
2011
Boyer Frédéric | Sagot Marie-France | Deniélou Yves-Pol | Viari Alain
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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 - <smcaps>I</smcaps>-ADH<smcaps>O</smcaps>R<smcaps>E</smcaps> - 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.</p>
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