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

DOI10.1007/S00285-016-0982-8zbMATH Open1354.42009arXiv1504.02367OpenAlexW3101164530WikidataQ40357196 ScholiaQ40357196MaRDI QIDQ728537FDOQ728537

Authors: Changchuan Yin, Jiasong Wang 

Publication date: 20 December 2016

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

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.

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

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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)

Cites Work

• Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence
• A new method to cluster DNA sequences using Fourier power spectrum
• An improved model for whole genome phylogenetic analysis by Fourier transform
• Information decomposition method to analyze symbolical sequences
• A measure of DNA sequence similarity by Fourier transform with applications on hierarchical clustering
• Some features of Fourier spectrum for symbolic sequences
• A converse coding theorem for mismatched decoding at the output of binary-input memoryless channels
• Detection and visualization of tandem repeats in dna sequences

Cited In (5)

• Investigating some attributes of periodicity in DNA sequences via semi-Markov modelling
• Chromosome-specific spatial periodicities in gene expression revealed by spectral analysis
• Latent periodicity-2 in coronavirus SARS-CoV-2 genome: evolutionary implications
• Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences
• Identification of repeats in DNA sequences using nucleotide distribution uniformity

Uses Software

• Matlab
• PPS
• lobSTR

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