| Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. | |
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MedLine Citation:
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PMID: 20623275 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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We discuss the importance of non-reversible evolutionary models when analyzing context-dependence. Given the inherent non-reversible nature of the well-known CpG-methylation-deamination process in mammalian evolution, non-reversible context-dependent evolutionary models may be well able to accurately model such a process. In particular, the lack of constraints on non-reversible substitution models might allow for more accurate estimation of context-dependent substitution parameters. To demonstrate this, we have developed different time-homogeneous context-dependent evolutionary models to analyze a large genomic dataset of primate ancestral repeats based on existing independent evolutionary models. We have calculated the difference in model fit for each of these models using Bayes Factors obtained via thermodynamic integration. We find that non-reversible context-dependent models can drastically increase model fit when compared to independent models and this on two primate non-coding datasets. Further, we show that further improvements are possible by clustering similar parameters across contexts. |
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Authors:
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Guy Baele; Yves Van de Peer; Stijn Vansteelandt |
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Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2010-07-11 |
Journal Detail:
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Title: Journal of molecular evolution Volume: 71 ISSN: 1432-1432 ISO Abbreviation: J. Mol. Evol. Publication Date: 2010 Jul |
Date Detail:
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Created Date: 2010-07-23 Completed Date: 2010-10-27 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0360051 Medline TA: J Mol Evol Country: Germany |
Other Details:
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Languages: eng Pagination: 34-50 Citation Subset: IM |
Affiliation:
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Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. gubae@psb.vib-ugent.be |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Animals Evolution* Humans Models, Theoretical* Primates Principal Component Analysis Pseudogenes / genetics Thermodynamics |
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