A benchmark of parametric methods for horizontal transfers detection.

Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different metho...

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Autores principales:	Jennifer Becq, Cécile Churlaud, Patrick Deschavanne
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2c2d902d63ad4ec5b0e84390cf408ee2
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id	oai:doaj.org-article:2c2d902d63ad4ec5b0e84390cf408ee2
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spelling	oai:doaj.org-article:2c2d902d63ad4ec5b0e84390cf408ee22021-11-25T06:24:54ZA benchmark of parametric methods for horizontal transfers detection.1932-620310.1371/journal.pone.0009989https://doaj.org/article/2c2d902d63ad4ec5b0e84390cf408ee22010-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20376325/?tool=EBIhttps://doaj.org/toc/1932-6203Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity.Jennifer BecqCécile ChurlaudPatrick DeschavannePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 4, p e9989 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jennifer Becq Cécile Churlaud Patrick Deschavanne A benchmark of parametric methods for horizontal transfers detection.
description	Horizontal gene transfer (HGT) has appeared to be of importance for prokaryotic species evolution. As a consequence numerous parametric methods, using only the information embedded in the genomes, have been designed to detect HGTs. Numerous reports of incongruencies in results of the different methods applied to the same genomes were published. The use of artificial genomes in which all HGT parameters are controlled allows testing different methods in the same conditions. The results of this benchmark concerning 16 representative parametric methods showed a great variety of efficiencies. Some methods work very poorly whatever the type of HGTs and some depend on the conditions or on the metrics used. The best methods in terms of total errors were those using tetranucleotides as criterion for the window methods or those using codon usage for gene based methods and the Kullback-Leibler divergence metric. Window methods are very sensitive but less specific and detect badly lone isolated gene. On the other hand gene based methods are often very specific but lack of sensitivity. We propose using two methods in combination to get the best of each category, a gene based one for specificity and a window based one for sensitivity.
format	article
author	Jennifer Becq Cécile Churlaud Patrick Deschavanne
author_facet	Jennifer Becq Cécile Churlaud Patrick Deschavanne
author_sort	Jennifer Becq
title	A benchmark of parametric methods for horizontal transfers detection.
title_short	A benchmark of parametric methods for horizontal transfers detection.
title_full	A benchmark of parametric methods for horizontal transfers detection.
title_fullStr	A benchmark of parametric methods for horizontal transfers detection.
title_full_unstemmed	A benchmark of parametric methods for horizontal transfers detection.
title_sort	benchmark of parametric methods for horizontal transfers detection.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/2c2d902d63ad4ec5b0e84390cf408ee2
work_keys_str_mv	AT jenniferbecq abenchmarkofparametricmethodsforhorizontaltransfersdetection AT cecilechurlaud abenchmarkofparametricmethodsforhorizontaltransfersdetection AT patrickdeschavanne abenchmarkofparametricmethodsforhorizontaltransfersdetection AT jenniferbecq benchmarkofparametricmethodsforhorizontaltransfersdetection AT cecilechurlaud benchmarkofparametricmethodsforhorizontaltransfersdetection AT patrickdeschavanne benchmarkofparametricmethodsforhorizontaltransfersdetection
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A benchmark of parametric methods for horizontal transfers detection.

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