ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

M. Vos; T.A.H. Beek; M.A. van Driel; M.A. Huynen; A. Eyre-Walker; M.W.J. van Passel

doi:10.1371/journal.pone.0062447

ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

M. Vos, T.A.H. Beek, M.A. van Driel, M.A. Huynen, A. Eyre-Walker, M.W.J. van Passel

Research output: Contribution to journal › Article › Academic › peer-review

8 Citations (Scopus)

Abstract

Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl

Original language	English
Article number	e62447
Journal	PLoS ONE
Volume	8
Issue number	5
DOIs	https://doi.org/10.1371/journal.pone.0062447
Publication status	Published - 2013

Keywords

positive selection
evolution
recombination
drosophila
campylobacter

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title = "ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes",

abstract = "Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl",

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AU - Vos, M.

AU - Beek, T.A.H.

AU - van Driel, M.A.

AU - Huynen, M.A.

AU - Eyre-Walker, A.

AU - van Passel, M.W.J.

PY - 2013

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AB - Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl

KW - positive selection

KW - evolution

KW - recombination

KW - drosophila

KW - campylobacter

U2 - 10.1371/journal.pone.0062447

DO - 10.1371/journal.pone.0062447

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IS - 5

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ER -

ODoSE: A Webserver for Genome-Wide Calculation of Adaptive Divergence in Prokaryotes

Abstract

Keywords

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