Markovianness and conditional independence in annotated bacterial DNA

DOI10.1515/SAGMB-2014-0002zbMATH Open1302.92069arXiv1311.4411OpenAlexW2218349704WikidataQ50994696 ScholiaQ50994696MaRDI QIDQ482822FDOQ482822

Authors: Servet Martínez, A. Hart 

Publication date: 6 January 2015

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

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.

Full work available at URL: https://arxiv.org/abs/1311.4411

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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)

Cites Work

• On Information and Sufficiency
• On a measure of lack of fit in time series models
• Title not available (Why is that?)
• Title not available (Why is that?)
• Statistical testing of Chargaff's second parity rule in bacterial genome sequences

Cited In (4)

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

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