  Chargaff's second parity rule for short oligonucleotides states that the
frequency of any short nucleotide sequence on a strand is approximately equal
to the frequency of its reverse complement on the same strand. Recent studies
have shown that, with the exception of organellar DNA, this parity rule
generally holds for double stranded DNA genomes and fails to hold for
single-stranded genomes. While Chargaff's first parity rule is fully explained
by the Watson-Crick pairing in the DNA double helix, a definitive explanation
for the second parity rule has not yet been determined. In this work, we
propose a model based on a hidden Markov process for approximating the
distributional structure of primitive DNA sequences. Then, we use the model to
provide another possible theoretical explanation for Chargaff's second parity
rule, and to predict novel distributional aspects of bacterial DNA sequences.
