KCM: a novel mechanistic codon model with increased control over codon substitution rates

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• Zaheri, M (Lausanne)
• Monday 20 June 2011, 16:10-16:30
• Seminar Room 1, Newton Institute.

If you have a question about this talk, please contact Mustapha Amrani.

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Models of codon evolution have attracted particular interest because of their unique abilities to detect selection forces acting on protein coding sequences. Here, we present a novel approach to model codon evolution using a matrix operator called Kronecker product. In particular, the 61 by 61 transition rate matrix of codon models is implemented using Kronecker product of three 4 by 4 nucleotide transition weigh matrices, which are the building blocks of codons. This mechanistic model generalizes current models of codon evolution while restricting the parameter space to 19 parameters (3 times 6 for each nucleotide transition matrix and one selection parameter) through the use of Kronecker product. AIC measures showed that our models had a better fit than current codon models on several data sets from mammals and plants. It is capable to better explain the biological complexity of protein coding gene evolution, and in particular can take into account multiple substitutions per codon. Finally, we applied this new model to the detection of positive selection and we show that the model is more accurate in estimating selection pressure when compared to previous codon models.

This talk is part of the Isaac Newton Institute Seminar Series series.

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