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Bacterial syntenies: an exact approach with gene quorum

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 spec...

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Autores principales: Deniélou, Yves-Pol, Sagot, Marie-France, Boyer, Frédéric, Viari, Alain
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121647/
https://www.ncbi.nlm.nih.gov/pubmed/21605461
http://dx.doi.org/10.1186/1471-2105-12-193
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author Deniélou, Yves-Pol
Sagot, Marie-France
Boyer, Frédéric
Viari, Alain
author_facet Deniélou, Yves-Pol
Sagot, Marie-France
Boyer, Frédéric
Viari, Alain
author_sort Deniélou, Yves-Pol
collection PubMed
description 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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spelling pubmed-31216472011-06-24 Bacterial syntenies: an exact approach with gene quorum Deniélou, Yves-Pol Sagot, Marie-France Boyer, Frédéric Viari, Alain BMC Bioinformatics Research Article 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. BioMed Central 2011-05-24 /pmc/articles/PMC3121647/ /pubmed/21605461 http://dx.doi.org/10.1186/1471-2105-12-193 Text en Copyright ©2011 Deniélou et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Deniélou, Yves-Pol
Sagot, Marie-France
Boyer, Frédéric
Viari, Alain
Bacterial syntenies: an exact approach with gene quorum
title Bacterial syntenies: an exact approach with gene quorum
title_full Bacterial syntenies: an exact approach with gene quorum
title_fullStr Bacterial syntenies: an exact approach with gene quorum
title_full_unstemmed Bacterial syntenies: an exact approach with gene quorum
title_short Bacterial syntenies: an exact approach with gene quorum
title_sort bacterial syntenies: an exact approach with gene quorum
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121647/
https://www.ncbi.nlm.nih.gov/pubmed/21605461
http://dx.doi.org/10.1186/1471-2105-12-193
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