ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes

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 subst...

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Bibliographic Details
Published inPloS one Vol. 8; no. 5; p. e62447
Main Authors Vos, Michiel, te Beek, Tim A H, van Driel, Marc A, Huynen, Martijn A, Eyre-Walker, Adam, van Passel, Mark W J
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 06.05.2013
Public Library of Science (PLoS)
Subjects
Adaptation
Adaptation, Biological - genetics
Algorithms
Analysis
Archaea - genetics
Bacteria
Bacteria - genetics
Bioinformatics
Biology
Campylobacter
Computer Science
Divergence
Drosophila
E coli
Escherichia coli
evolution
Evolution & development
Evolution, Molecular
Galaxies
Genes
Genetic aspects
Genome, Archaeal
Genome, Bacterial
Genomes
Genomics
Informatics
Insects
Internet
Mathematical analysis
Mitochondrial DNA
Models, Genetic
Mutation
Neutrality
Polymorphism, Genetic
positive selection
Prokaryotes
Proteins
recombination
Salmonella
Sequence Analysis, DNA
Software
Taxa
Trends
Netherlands
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Summary: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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Competing Interests: MWJvP is a PLOS ONE Editorial Board member. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.
Conceived and designed the experiments: MV MWJvP. Performed the experiments: MV TtB MWJvP. Analyzed the data: MV TtB MAvD MAH AEW MWJvP. Contributed reagents/materials/analysis tools: MV TtB MAvD MAH AEW MWJvP. Wrote the paper: MV MWJvP.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0062447