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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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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. |
format | Online Article Text |
id | pubmed-3121647 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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