Spectral sum rules and search for periodicities in DNA sequences

DOI10.1016/J.PHYSLETA.2011.03.007MaRDI QIDQ434008zbMATH OpenOpenAlexFDO

Authors Vladimir R. Chechetkin

Publication date 9 July 2012

Published in Physics Letters. A (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1104.0541

zbMATH Keywords

Fourier transformsRayleigh distributionDe Finetti distributionlatent periodicities

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Numerical methods for discrete and fast Fourier transforms (65T50)

Abstract: Periodic patterns play the important regulatory and structural roles in genomic DNA sequences. Commonly, the underlying periodicities should be understood in a broad statistical sense, since the corresponding periodic patterns have been strongly distorted by the random point mutations and insertions/deletions during molecular evolution. The latent periodicities in DNA sequences can be efficiently displayed by Fourier transform. The criteria of significance for observed periodicities are obtained via the comparison versus the counterpart characteristics of the reference random sequences. We show that the restrictions imposed on the significance criteria by the rigorous spectral sum rules can be rationally described with De Finetti distribution. This distribution provides the convenient intermediate asymptotic form between Rayleigh distribution and exact combinatoric theory.

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Cites work

• scientific article; zbMATH DE number 3349081 (Why is no real title available?)
• On the spectral criteria of disorder in nonperiodic sequences: application to inflation models, symbolic dynamics and DNA sequences
• Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence
• Spectral entropy criteria for structural segmentation in genomic DNA sequences

Cited in

(5)

• Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences
• Spectral entropy criteria for structural segmentation in genomic DNA sequences
• Statistics of genome architecture
• Periodic power spectrum with applications in detection of latent periodicities in DNA sequences
• Large-scale chromosome folding versus genomic DNA sequences: a discrete double Fourier transform technique

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