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dc.contributor.authorAngelis, Ken_US
dc.contributor.authorDos Reis, Men_US
dc.contributor.authorYang, Zen_US
dc.date.accessioned2016-05-10T15:40:54Z
dc.date.issued2014-07en_US
dc.date.submitted2016-05-04T17:19:37.271Z
dc.identifier.urihttp://qmro.qmul.ac.uk/xmlui/handle/123456789/12250
dc.description.abstractThe nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the d(N)/d(S) ratio using two sequences. Both heuristic counting methods and the maximum-likelihood (ML) method based on a codon substitution model are widely used for such analysis. However, these methods do not have nice statistical properties, as the estimates can be zero or infinity in some data sets, so that their means and variances are infinite. In large genome-scale comparisons, such extreme estimates (either 0 or ∞) of ω and sequence distance (t) are common. Here, we implement a Bayesian method to estimate ω and t in pairwise sequence comparisons. Using a combination of computer simulation and real data analysis, we show that the Bayesian estimates have better statistical properties than the ML estimates, because the prior on ω and t shrinks the posterior of those parameters away from extreme values. We also calculate the posterior probability for ω > 1 as a Bayesian alternative to the likelihood ratio test. The new method is computationally efficient and may be useful for genome-scale comparisons of protein-coding gene sequences.en_US
dc.format.extent1902 - 1913en_US
dc.languageengen_US
dc.language.isoenen_US
dc.relation.ispartofMol Biol Evolen_US
dc.rightsCC-BY
dc.subjectBayesian estimationen_US
dc.subjectevolutionary distanceen_US
dc.subjectnonsynonymous/synonymous rate ratioen_US
dc.subjectpairwise comparisonsen_US
dc.subjectprotein-coding sequencesen_US
dc.subjectAlgorithmsen_US
dc.subjectAnimalsen_US
dc.subjectBayes Theoremen_US
dc.subjectComputer Simulationen_US
dc.subjectGenomeen_US
dc.subjectHumansen_US
dc.subjectMammalsen_US
dc.subjectSelection, Geneticen_US
dc.subjectSequence Alignmenten_US
dc.titleBayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.en_US
dc.typeArticle
dc.rights.holder© 2014 The Author
dc.identifier.doi10.1093/molbev/msu142en_US
pubs.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/24748652en_US
pubs.issue7en_US
pubs.notesNot knownen_US
pubs.publication-statusPublisheden_US
pubs.volume31en_US


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