A nucleotide substitution model with nearest-neighbour interactions | Zendy

Gerton Lunter | Zendy; Jotun Hein | Zendy

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A nucleotide substitution model with nearest-neighbour interactions

Author(s) -

Gerton Lunter,

Jotun Hein

Publication year - 2004

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/bth901

Subject(s) - substitution (logic) , cpg site , nucleotide , inference , context (archaeology) , bayesian probability , computer science , algorithm , computational biology , biology , biological system , genetics , artificial intelligence , gene , dna methylation , paleontology , gene expression , programming language

It is well known that neighbouring nucleotides in DNA sequences do not mutate independently of each other. In this paper, we introduce a context-dependent substitution model and derive an algorithm to calculate the likelihood of sequences evolving under this model. We use this algorithm to estimate neighbour-dependent substitution rates, as well as rates for dinucleotide substitutions, using a Bayesian sampling procedure. The model is irreversible, giving an arrow to time, and allowing the position of the root between a pair of sequences to be inferred without using out-groups.

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