Markovianness and Conditional Independence in Annotated Bacterial DNA

TL;DR

This paper investigates the probabilistic structure of bacterial DNA, revealing Markovian properties at gene boundaries and a conditional independence that enables unique modeling, with implications for understanding genomic organization.

Contribution

It demonstrates the presence of Markovianness and a unique Markov chain structure in bacterial genome annotations, linking it to Chargaff's parity rule.

Findings

Markovian structure at gene boundary regions

Conditional independence property of START and STOP codons

Compliance with Chargaff's second parity rule at the codon level

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, the annotated sequence is shown to comply with Chargaff's second parity rule at the codon level.