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A new method to study genome mutations using the information entropy

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  • Vopson, Melvin M.
  • Robson, Samuel C.

Abstract

We report a non-clinical, mathematical method of studying genetic sequences based on the information theory. Our method involves calculating the information entropy spectrum of genomes by splitting them into “windows” containing a fixed number of nucleotides. The information entropy value of each window is computed using the m-block information entropy formula. We show that the information entropy spectrum of genomes contains sufficient information to allow detection of genetic mutations, as well as possibly predicting future ones. Our study indicates that the best m-block size is 2 and the optimal window size should contain more than 9, and less than 33 nucleotides. In order to implement the proposed technique, we created specialized software, which is freely available. Here we report the successful test of this method on the reference RNA sequence of the SARS-CoV-2 virus collected in Wuhan, Dec. 2019 (MN908947) and one of its randomly selected variants from Taiwan, Feb. 2020 (MT370518), displaying 7 mutations.

Suggested Citation

  • Vopson, Melvin M. & Robson, Samuel C., 2021. "A new method to study genome mutations using the information entropy," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 584(C).
    • Handle: RePEc:eee:phsmap:v:584:y:2021:i:c:s0378437121006567
    DOI: 10.1016/j.physa.2021.126383
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    References listed on IDEAS

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    1. Fan Wu & Su Zhao & Bin Yu & Yan-Mei Chen & Wen Wang & Zhi-Gang Song & Yi Hu & Zhao-Wu Tao & Jun-Hua Tian & Yuan-Yuan Pei & Ming-Li Yuan & Yu-Ling Zhang & Fa-Hui Dai & Yi Liu & Qi-Min Wang & Jiao-Jiao , 2020. "A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 579(7798), pages 265-269, March.
    2. Thanos, Dimitrios & Li, Wentian & Provata, Astero, 2018. "Entropic fluctuations in DNA sequences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 493(C), pages 444-457.
    3. J. A. Tenreiro Machado, 2012. "Shannon Entropy Analysis of the Genome Code," Mathematical Problems in Engineering, Hindawi, vol. 2012, pages 1-12, May.
    4. Fan Wu & Su Zhao & Bin Yu & Yan-Mei Chen & Wen Wang & Zhi-Gang Song & Yi Hu & Zhao-Wu Tao & Jun-Hua Tian & Yuan-Yuan Pei & Ming-Li Yuan & Yu-Ling Zhang & Fa-Hui Dai & Yi Liu & Qi-Min Wang & Jiao-Jiao , 2020. "Author Correction: A new coronavirus associated with human respiratory disease in China," Nature, Nature, vol. 580(7803), pages 7-7, April.
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