Periodic power spectrum with applications in detection of latent periodicities in DNA sequences
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Publication:728537
DOI10.1007/S00285-016-0982-8zbMATH Open1354.42009arXiv1504.02367OpenAlexW3101164530WikidataQ40357196 ScholiaQ40357196MaRDI QIDQ728537FDOQ728537
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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Cites Work
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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
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