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

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Abstract

Periodic elements play important roles in genomic structures and functions, yet some complex periodic elements in genomes are difficult to detect by conventional methods such as digital signal processing and statistical analysis. We propose a periodic power spectrum (PPS) method for analyzing periodicities of DNA sequences. The PPS method employs periodic nucleotide distributions of DNA sequences and directly calculates power spectra at specific periodicities. The magnitude of a PPS reflects the strength of a signal on periodic positions. In comparison with Fourier transform, the PPS method avoids spectral leakage, and reduces background noise that appears high in Fourier power spectrum. Thus, the PPS method can effectively capture hidden periodicities in DNA sequences. Using a sliding window approach, the PPS method can precisely locate periodic regions in DNA sequences. We apply the PPS method for detection of hidden periodicities in different genome elements, including exons, microsatellite DNA sequences, and whole genomes. The results show that the PPS method can minimize the impact of spectral leakage and thus capture true hidden periodicities in genomes. In addition, performance tests indicate that the PPS method is more effective and efficient than a fast Fourier transform. The computational complexity of the PPS algorithm is \(\mathrm{O}(N)\). Therefore, the PPS method may have a broad range of applications in genomic analysis. The MATLAB programs for implementing the PPS method are available from MATLAB Central (http://www.mathworks.com/matlabcentral/fileexchange/55298).

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Acknowledgments

We are grateful to Professor Donald Morrison for helpful discussion, and to the anonymous reviewers for their valuable comments. We thank Emily Yin from Fremd high school for proof reading of the paper.

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Authors and Affiliations

  1. Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL, 60607-7045, USA

    Changchuan Yin

  2. Department of Mathematics, Nanjing University, Nanjing, Jiangsu, 210093, China

    Jiasong Wang

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  1. Changchuan Yin
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  2. Jiasong Wang
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Correspondence to Changchuan Yin.

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Yin, C., Wang, J. Periodic power spectrum with applications in detection of latent periodicities in DNA sequences. J. Math. Biol. 73, 1053–1079 (2016). https://doi.org/10.1007/s00285-016-0982-8

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  • DOI: https://doi.org/10.1007/s00285-016-0982-8

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