Models Applied to DNA Sequences with Multinomial Correlated Responses

Multinomial multivariate models are proposed to describe the codon frequencies in DNA sequences, as well as the order and frequency that nucleotide bases have in each codon considering the dependence among the bases inside a codon. Logistic regressive models are used with different dependence structures on the three codon positions. Also, multinomialextensions of the Bahadur’s representation are proposed to model correlated multinomial data. An application of these models to the NADH4 gene from human mitochondrial genome is presented. AIC, BIC and the leave-one-out cross validation are employed to compare the various models peformance.