Markovianness and conditional independence in annotated bacterial DNA.

Abstract

We explore the probabilistic structure of DNA in a number of bacterial genomes and conclude that a form of Markovianness is present at the boundaries between coding and non-coding regions, that is, the sequence of START and STOP codons annotated for the bacterial genome. This sequence is shown to satisfy a conditional independence property which allows its governing Markov chain to be uniquely identified from the abundances of START and STOP codons. Furthermore, we show that the annotated sequence of STARTs and STOPs complies with Chargaff's second parity rule.