Periodic power spectrum with applications in detection of latent periodicities in DNA sequences

DOI10.1007/S00285-016-0982-8MaRDI QIDQ728537zbMATH OpenOpenAlexWikidataFDO

Authors Changchuan Yin, Jiasong Wang

Publication date 20 December 2016

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1504.02367

zbMATH Keywords

Fourier transformperiodicityspectral leakageDNA genomeperiodic power spectrum

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Fourier and Fourier-Stieltjes transforms and other transforms of Fourier type (42A38)

Abstract: Latent periodic elements in genomes play important roles in genomic functions. Many complex periodic elements in genomes are difficult to be detected by commonly used digital signal processing (DSP). We present a novel method to compute the periodic power spectrum of a DNA sequence based on the nucleotide distributions on periodic positions of the sequence. The method directly calculates full periodic spectrum of a DNA sequence rather than frequency spectrum by Fourier transform. The magnitude of the periodic power spectrum reflects the strength of the periodicity signals, thus, the algorithm can capture all the latent periodicities in DNA sequences. We apply this method on detection of latent periodicities in different genome elements, including exons and microsatellite DNA sequences. The results show that the method minimizes the impact of spectral leakage, captures a much broader latent periodicities in genomes, and outperforms the conventional Fourier transform.

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Cites work

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• A new method to cluster DNA sequences using Fourier power spectrum
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Cited in

(7)

• Investigating some attributes of periodicity in DNA sequences via semi-Markov modelling
• Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences
• The problem of power spectrum and the signal-to-noise ratio and its fast algorithm implementation in gene identification
• Latent periodicity-2 in coronavirus SARS-CoV-2 genome: evolutionary implications
• Chromosome-specific spatial periodicities in gene expression revealed by spectral analysis
• Identification of repeats in DNA sequences using nucleotide distribution uniformity
• Spectral sum rules and search for periodicities in DNA sequences

Describes a project that uses

Uses Software

• Matlab
• PPS
• lobSTR

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