ArticleBMC bioinformatics2011
Bacterial syntenies: an exact approach with gene quorum.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes.Chemical reviews · 2024Review
- Pan-genome analyses of model fungal species.Microbial genomics · 2019Article
- CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts.BMC bioinformatics · 2019Article
- Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators.Scientific reports · 2017Article
- Finding approximate gene clusters with Gecko 3.Nucleic acids research · 2016Article
- Revealing the hidden functional diversity of an enzyme family.Nature chemical biology · 2014Article
- SyntTax: a web server linking synteny to prokaryotic taxonomy.BMC bioinformatics · 2013Article
- PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species.Nucleic acids research · 2012Article
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4 authors.
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Abstract
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-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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