Markovianness and conditional independence in annotated bacterial DNA

DOI10.1515/SAGMB-2014-0002MaRDI QIDQ482822zbMATH OpenOpenAlexWikidataFDO

Authors Servet Martínez, A. Hart

Publication date 6 January 2015

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1311.4411, http://hdl.handle.net/10533/148149

zbMATH Keywords

Markov chainKullback-Leibler divergenceconditional independencebacteriaChargaff's second parity rule

Mathematics Subject Classification ID

Nonparametric hypothesis testing (62G10) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Non-Markovian processes: hypothesis testing (62M07)

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.

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Cites work

• scientific article; zbMATH DE number 3143969 (Why is no real title available?)
• scientific article; zbMATH DE number 3544999 (Why is no real title available?)
• On Information and Sufficiency
• On a measure of lack of fit in time series models
• Statistical testing of Chargaff's second parity rule in bacterial genome sequences

Cited in

(4)

• A stationary distribution associated to a set of laws whose initial states are grouped into classes. An application in genomics
• Statistical testing of Chargaff's second parity rule in bacterial genome sequences
• In-phase implies large likelihood for independent codon model: distinguishing coding from non-coding sequences
• A Gibbs approach to Chargaff's second parity rule

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