A Gibbs approach to Chargaff's second parity rule

DOI10.1007/S10955-011-0377-6MaRDI QIDQ664592zbMATH OpenOpenAlexFDO

Authors Servet Martínez, Felipe Olmos, A. Hart

Publication date 2 March 2012

Published in Journal of Statistical Physics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1105.0685

zbMATH Keywords

central limit theoremGibbs measureChargaff's parity rulesreverse complementary relation

Mathematics Subject Classification ID

Parametric hypothesis testing (62F03) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10) Central limit and other weak theorems (60F05) Statistical mechanics of polymers (82D60)

Abstract: Chargaff's second parity rule (CSPR) asserts that the frequencies of short polynucleotide chains are the same as those of the complementary reversed chains. Up to now, this hypothesis has only been observed empirically and there is currently no explanation for its presence in DNA strands. Here we argue that CSPR is a probabilistic consequence of the reverse complementarity between paired strands, because the Gibbs distribution associated with the chemical energy between the bonds satisfies CSPR. We develop a statistical test to study the validity of CSPR under the Gibbsian assumption and we apply it to a large set of bacterial genomes taken from the GenBank repository.

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Cites work

• Central limit asymptotics for shifts of finite type
• Equilibrium states and the ergodic theory of Anosov diffeomorphisms
• Statistical testing of Chargaff's second parity rule in bacterial genome sequences

Cited in

(6)

• A nucleotide composition constraint of genome sequences
• Novel look at DNA and life -- symmetry as evolutionary forcing
• The breakdown of the word symmetry in the human genome
• Genomic compliance with Chargaff's second parity rule may have originated non-adaptively, but stem-loops now function adaptively
• Local symmetry of non-coding genetic sequences
• Statistical testing of Chargaff's second parity rule in bacterial genome sequences

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