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The Danish National Research Foundation:
Network in Mathematical Physics and Stochastics

Funded by The Danish National Research Foundation

MPS-RR 2004-29
December 2004

Pseudo-likelihood analysis of context-dependent codon substitution models

by: Ole F. Christensen , Asger Hobolth , Jens Ledet Jensen


We consider Markov processes for coding DNA sequence evolution. In context dependent models the instantaneous substitution rate for a codon depends on the neighboring codons. This makes the model analytically intractable, and previously Markov chain Monte Carlo methods have been used for statistical inference. We introduce an approximative estimation method based on pseudo-likelihood that makes inference analytically tractable. We demonstrate that the pseudo-likelihood estimates are very accurate, and from analyzing 348 human-mouse coding sequences we conclude that incorporating the CpG effect improves the model fits considerably.

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