Journal
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
Volume 584, Issue -, Pages -Publisher
ELSEVIER
DOI: 10.1016/j.physa.2021.126383
Keywords
Information Entropy Spectra; DNA sequence; RNA sequence; Detection of genetic mutations
Categories
Funding
- School of Mathematics and Physics, University of Portsmouth, UK
- Research England's Expanding Excellence in England (E3) Fund
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A non-clinical, mathematical method based on information theory is proposed to study genetic sequences, involving calculating the information entropy spectrum of genomes to detect genetic mutations and possibly predict future ones. The optimal m-block size is 2, and the optimal window size contains more than 9 and less than 33 nucleotides. The method was successfully tested on the reference RNA sequence of the SARS-CoV-2 virus and one of its variants from Taiwan, displaying 7 mutations.
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. (C) 2021 Elsevier B.V. All rights reserved.
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