Bacterial syntenies: an exact approach with gene quorum

BMC Bioinformatics

Research Article

Yves-Pol Deniélou¹  Alain Viari¹  Marie-France Sagot²  Frédéric Boyer³ 

[1] INRIA Grenoble-Rhône-Alpes, team BAMBOO, 655 avenue de l’Europe, 38334, Montbonnot Cedex, France;INRIA Grenoble-Rhône-Alpes, team BAMBOO, 655 avenue de l’Europe, 38334, Montbonnot Cedex, France;Université de Lyon, Lyon; Université Lyon 1; CNRS, UMR5558, F-69000, France;UMR754 INRA, Université de Lyon 1, 50 Avenue Tony Garnier, 69007, Lyon, France;

关键词: Gene Order;    Interval Graph;    Depth First Search;    Primary Graph;    Synteny Block;   

DOI  :  10.1186/1471-2105-12-193

 received in 2011-01-24, accepted in 2011-05-24,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsIn 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.ConclusionsWe 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-ADHO RE - 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.

【 授权许可】

CC BY   
© Deniélou et al; licensee BioMed Central Ltd. 2011