title: A model capturing novel strand symmetries in bacterial DNA.
abstract: 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.
authors.affiliation: Departamento de Matemática, Universidade Federal de Santa Catarina, Brazil. sobottka@mtm.ufsc.br
authors.forename: Marcelo
authors.initials: M
authors.lastname: Sobottka
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Hart
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry*; D008390:Markov Chains; D008956:Models, Chemical
chemical_list: D004269:DNA, Bacterial