Is there an acceleration of the CpG transition rate during the mammalian radiation? | Zendy

Martin Peifer | Zendy; John Karro | Zendy; H. H. von Grünberg | Zendy

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Is there an acceleration of the CpG transition rate during the mammalian radiation?

Author(s) -

Martin Peifer,

John Karro,

H. H. von Grünberg

Publication year - 2008

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btn391

Subject(s) - substitution (logic) , cpg site , acceleration , markov chain , artifact (error) , reaction rate constant , constant (computer programming) , boundary (topology) , truncation (statistics) , dose rate , transition rate matrix , computer science , econometrics , statistical physics , biology , chemistry , statistics , kinetics , physics , mathematics , genetics , artificial intelligence , radiochemistry , mathematical analysis , gene expression , classical mechanics , quantum mechanics , dna methylation , gene , programming language

In this article we build a model of the CpG dinucleotide substitution rate and use it to challenge the claim that, that rate underwent a sudden mammalian-specific increase approximately 90 million years ago. The evidence supporting this hypothesis comes from the application of a model of neutral substitution rates able to account for elevated CpG dinucleotide substitution rates. With the initial goal of improving that model's accuracy, we introduced a modification enabling us to account for boundary effects arising by the truncation of the Markov field, as well as improving the optimization procedure required for estimating the substitution rates.

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