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Information analysis of the human DNA

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Abstract

The structure of the deoxyribonucleic acid (DNA) is quantified using an algorithm that translates the chromosome data into a state-space plot. This scheme converts the information written by means of the four nitrogenous bases {thymine, cytosine, adenine, guanine} into a two-dimensional numerical representation. The resulting locus is then analyzed in the perspective of fractal and information theories. The classical integer-order expressions, namely the entropy and mutual information of two-dimensional distributions, are compared with those obtained using recently proposed fractional formulations. It is verified that the fractional approach leads to a superior discrimination of the information embedded in the two-dimensional locus. The dataset is further explored through the Jensen–Shannon divergence and multidimensional scaling. The proposed approach is first applied to the 24 Human chromosomes. In a second phase, the Bonobo, Chimpanzee and Orangutan are also considered for establishing a comparison between the four species. The results shed some light upon the information content of the distinct chromosomes.

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Acknowledgements

The author thanks the following organizations for allowing access to genome data. Human: The Genome Reference Consortium, Common Chimpanzee: The Chimpanzee Sequencing and Analysis Consortium, Bonobo: Max Planck Institute for Evolutionary Anthropology, Orangutan: Genome Sequencing Center at WUSTL.

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  1. Department of Electrical Engineering, Institute of Engineering, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida, 431, 4249-015, Porto, Portugal

    J. Tenreiro Machado

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Machado, J.T. Information analysis of the human DNA. Nonlinear Dyn 98, 3169–3186 (2019). https://doi.org/10.1007/s11071-019-05066-7

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