A Markovian genomic concatenation model guided by persymmetric matrices

Abstract

The aim of this work is to provide a rigorous mathematical analysis of a stochastic concatenation model presented by Sobottka and Hart (2011) which allows approximation of the first-order stochastic structure in bacterial DNA by means of a stationary Markov chain. Two probabilistic constructions that rigorously formalize the model are presented. Necessary and sufficient conditions for a Markov chain to be generated by the model are given, as well as the theoretical background needed for designing new algorithms for statistical analyses of real bacterial genomes. It is shown that the model encompasses the Markov chains satisfying intra-strand parity, a property observed in most DNA sequences.