Markovianness and conditional independence in annotated bacterial DNA

Hart Andrew () and Martínez Servet
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Hart Andrew: Centro de Modelamiento Matemático, Universidad de Chile, Beauchef 851, Santiago, Chile
Martínez Servet: Centro de Modelamiento Matemático and Departamento de Ingeniería Matemática, Universidad de Chile, Beauchef 851, Santiago, Chile

Statistical Applications in Genetics and Molecular Biology, 2014, vol. 13, issue 6, 693-716

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.

Keywords: bacteria; Chargaff’s second parity rule; conditional independence; Kullback-Leibler divergence; Markov chain (search for similar items in EconPapers)
Date: 2014
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DOI: 10.1515/sagmb-2014-0002

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