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Fractional order description of DNA. (English) Zbl 1443.92142

Summary: This study addresses the deoxyribonucleic acid (DNA) and proposes a procedure based on the association of statistics, information theory, signal processing, Fourier analysis and fractional calculus for describing fundamental characteristics of the DNA. In a first phase the 24 chromosomes of the Human are evaluated. In a second phase, 10 chromosomes for different species are also processed and the results compared. The results reveal invariance in the description and close resemblances with fractional Brownian motion.

MSC:

92D20 Protein sequences, DNA sequences

Software:

Genocop
Full Text: DOI

References:

[1] Kolmogorov, A. N., Wienersche spiralen und einige andere interessante kurven im hilbertschen raum, C. R. (Dokl.) Acad. Sci. URSS, 26, 2, 115-118 (1940) · JFM 66.0552.03
[2] Mandelbrot, B. B.; Ness, J. W.V., The fractional Brownian motions, fractional noises and applications, SIAM Rev., 10, 4, 422-437 (1968) · Zbl 0179.47801
[3] Keshner, M. S., \(1 / f\) noise, Proc. IEEE, 70, 3, 212-218 (1982)
[4] Mandelbrot, B. B., The Fractal Geometry of Nature (1983), W.H. Freeman: W.H. Freeman New York · Zbl 1194.30028
[5] Nourdin, I., Selected Aspects of Fractional Brownian Motion (2012), Springer: Springer Milan · Zbl 1274.60006
[6] Lo, A. W., Long term memory in stock market prices, Econometrica, 59, 5, 1279-1313 (1991) · Zbl 0781.90023
[7] Baillie, R. T., Long memory processes and fractional integration in econometrics, J. Econometrics, 73, 1, 5-59 (1996) · Zbl 0854.62099
[8] Király, A.; Jánosi, I. M., Stochastic modeling of daily temperature fluctuations, Phys. Rev. E, 65, 051102, 1-6 (1998)
[9] Montanari, A.; Rosso, R.; Taqqu, M. S., A seasonal fractional ARIMA model applied to the Nile river monthly flows at Aswan, Water Resour. Res., 36, 5, 1249-1259 (2000)
[10] Koutsoyiannis, D., Climate change, the hurst phenomenon, and hydrological statistics, Hydrol. Sci. J., 48, 1, 3-24 (2003)
[11] Li, C.-F., Rescaled-range and power spectrum analyses on well-logging data, Geophys. J. Int., 153, 1, 201-212 (2003)
[12] Chen, C.-C.; Lee, Y.-T.; Chang, Y.-F., A relationship between hurst exponents of slip and waiting time data of earthquakes, Physica A, 387, 18, 4643-4648 (2008)
[13] Vyushin, D. I.; Kushner, P. J.; Mayer, J., On the origins of temporal power-law behavior in the global atmospheric circulation, Geophys. Res. Lett., 36, 14, L14706 (2009)
[14] Voss, R. F.; Clarke, J., \(1 / f\) noise in music and speech, Nature, 258, 317-318 (1975)
[15] Voss, R. F.; Clarke, J., \(1 / f\) noise in music: Music from \(1 / f\) noise, J. Acoust. Soc. Am., 63, 1, 258-263 (1978)
[16] Ro, W.; Kwon, Y., \(1 / f\) noise analysis of songs in various genre of music, Chaos Solitons Fractals, 42, 4, 2305-2311 (2009)
[17] Peng, C. K.; Buldyrev, S.; Goldberger, A.; Havlin, S.; Sciortino, F.; Simons, M.; Stanley, H. E., Long-range correlations in nucleotide sequences, Nature, 356, 168-171 (1992)
[18] Peng, C.-K.; Buldyrev, S.; Havlin, S.; Simmons, M.; Stanley, H.; Goldberger, A., Mosaic organization of DNA nucleotides, Phys. Rev. E, 49, 2, 1685-1689 (1994)
[19] Voss, R. F., Evolution of long-range fractal correlation and \(1 / f\) noise in DNA base sequences, Phys. Rev. Lett., 68, 3805-3808 (1992)
[20] Som, A.; Chattopadhyay, S.; Chakraborth, J.; Bandyopadhyay, D., Codon distribution in DNA, Phys. Rev. E: Stat. Nonlinear Soft Matter Phys., 63, 5, 051908 (2001)
[21] Kim, J.; Kwon, Y.; Yang, S.; Lee, E., Codon and amino-acid distribution in DNA, Chaos Solitons Fractals, 23, 5, 1795-1807 (2005) · Zbl 1066.92023
[22] Ortigueira, M. D.; Batista, A. G., A fractional linear system view of the fractional Brownian motion, Nonlinear Dyn., 38, 1-4, 295-303 (2004) · Zbl 1115.60044
[23] Ortigueira, M. D.; Batista, A. G., On the relation between the fractional Brownian motion and the fractional derivatives, Phys. Lett. A, 372, 7, 958-968 (2008) · Zbl 1217.26016
[24] Deng, W.; Barkai, E., Ergodic properties of fractional Brownian-Langevin motion, Phys. Rev. E: Stat. Nonlinear Soft Matter Phys., 79, 1, 011112-1-011112-7 (2009)
[25] Grigolini, P.; Aquino, G.; Bologna, M.; Luković, M.; West, B. J., A theory of \(1 / f\) noise in human cognition, Physica A, 388, 19, 4192-4204 (2009)
[26] Machado, J. T.; Kiryakova, V.; Mainardi, F., Recent history of fractional calculus, Commun. Nonlinear Sci. Numer. Simul., 16, 3, 1140-1153 (2011) · Zbl 1221.26002
[27] Machado, J. T.; Galhano, A. M.; Trujillo, J. J., On development of fractional calculus during the last fifty years, Scientometrics, 98, 1, 577-582 (2014)
[28] Oldham, K.; Spanier, J., The Fractional Calculus: Theory and Application of Differentiation and Integration to Arbitrary Order (1974), Academic Press: Academic Press New York · Zbl 0292.26011
[29] Samko, S.; Kilbas, A.; Marichev, O., Fractional Integrals and Derivatives: Theory and Applications (1993), Gordon and Breach Science Publishers: Gordon and Breach Science Publishers Amsterdam · Zbl 0818.26003
[30] Miller, K.; Ross, B., An Introduction to the Fractional Calculus and Fractional Differential Equations (1993), John Wiley and Sons: John Wiley and Sons New York · Zbl 0789.26002
[31] Podlubny, I., Fractional differential equations, Volume 198: An Introduction to Fractional Derivatives, Fractional Differential Equations, to Methods of Their Solution, Mathematics in Science and Engineering (1998), Academic Press: Academic Press San Diego
[32] Kilbas, A.; Srivastava, H.; Trujillo, J., Theory and applications of fractional differential equations, (North-Holland Mathematics Studies, vol. 204 (2006), Elsevier: Elsevier Amsterdam) · Zbl 1092.45003
[33] Ortigueira, M. D.; Machado, J. A.T., Fractional signal processing and applications, Signal Process., 83, 11, 2285-2286 (2003)
[34] Magin, R., Fractional Calculus in Bioengineering (2006), Begell House Inc.: Begell House Inc. Redding
[35] Ortigueira, M. D.; Machado, J. A.T., Fractional calculus applications in signals and systems, Signal Process., 86, 10, 2503-2504 (2006) · Zbl 1172.94301
[36] Sabatier, J.; Agrawal, O. P.; Machado, J. T., Advances in Fractional Calculus: Theoretical Developments and Applications in Physics and Engineering (2007), Springer: Springer Dordrecht, The Netherlands · Zbl 1116.00014
[37] Ionescu, C.; Keyser, R. D., Relations between fractional-order model parameters and lung pathology in chronic obstructive pulmonary disease, IEEE Trans. Biomed. Eng., 56, 4, 978-987 (2009)
[38] Mainardi, F., Fractional Calculus and Waves in Linear Viscoelasticity: An Introduction to Mathematical Models (2010), Imperial College Press: Imperial College Press London · Zbl 1210.26004
[39] Ortigueira, M.; Machado, J. A.T.; Trujillo, J.; Vinagre, B., Advances in fractional signals and systems, Signal Process., 91, 3, 349 (2011)
[40] Baleanu, D.; Diethelm, K.; Scalas, E.; Trujillo, J. J., Fractional calculus: models and numerical methods, series on complexity, (Nonlinearity and Chaos (2012), World Scientific Publishing Company: World Scientific Publishing Company Singapore) · Zbl 1248.26011
[41] Ionescu, C. M., The Human Respiratory System. An Analysis of the Interplay between Anatomy, Structure, Breathing and Fractal Dynamics, (BioEngineering (2013), Springer: Springer Amsterdam) · Zbl 1273.92016
[42] Machado, J. T.; Galhano, A. M., Symbolic fractional dynamics, IEEE J. Emerging Sel. Top. Circuits Syst., 3, 3, 468-474 (2013)
[43] Machado, J. T., Fractional order generalized information, Entropy, 16, 4, 2350-2361 (2014)
[44] Machado, J. T.; Costa, A. C.; Quelhas, M. D., Fractional dynamics in DNA, Commun. Nonlinear Sci. Numer. Simul., 16, 8, 2963-2969 (2011) · Zbl 1218.92038
[45] Machado, J. T.; Costa, A.; Quelhas, M., Entropy analysis of DNA code dynamics in human chromosomes, Comput. Math. Appl., 62, 3, 1612-1617 (2011) · Zbl 1228.94032
[46] Pearson, H., Genetics: what is a gene?, Nature, 441, 7092, 398-401 (2006)
[47] Tiwari, S.; Ramachandran, S.; Bhattacharya, A.; Bhattacharya, S.; Ramaswamy, R., Prediction of probable genes by Fourier analysis of genomic sequences, Computer Appl. Biosci.: CABIOS, 13, 3, 263-270 (1997)
[48] Dodin, G.; Vandergheynst, P.; Levoir, P.; Cordier, C.; Marcourt, L., Fourier and wavelet transform analysis, a tool for visualizing regular patterns in DNA sequences, J. Theor. Biol., 206, 3, 323-326 (2000)
[49] Afreixo, V.; Ferreira, P. G.; Santos, D., Fourier analysis of symbolic data: a brief review, Digital Signal Process., 14, 6, 523-530 (2004)
[50] Afreixo, V.; Ferreira, P. G.; Santos, D., Spectrum and symbol distribution of nucleotide sequences, Phys. Rev. E, 70, 3, 03190.1-03190.4 (2004)
[51] Yin, C.; Yau, S. T., A Fourier characteristic of coding sequences: origins and a non-Fourier approximation, J. Comput. Biol., 12, 9, 1153-1165 (2005)
[53] Jeng, C.-C.; Yang, I.-C.; Hsieh, K.-L.; Lin, C.-N., Clustering analysis for bacillus genus using Fourier transform and self-organizing map, (King, I.; Wang, J.; Chan, L.-W.; Wang, D., Neural Information Processing (2006), Springer: Springer Berlin, Heidelberg), 48-57
[55] Shannon, C. E., A mathematical theory of communication, Bell Syst. Tech. J., 27, 3, 379-423 (1948), 623-656 · Zbl 1154.94303
[56] Gray, R. M., Entropy and Information Theory (2009), Springer-Verlag: Springer-Verlag New York
[57] Holland, J. H., Adaptation in Natural and Artificial Systems (1975), The University of Michigan Press: The University of Michigan Press Ann Arbor · Zbl 0317.68006
[58] Goldberg, D. E., Genetic Algorithms in Search Optimization, and Machine Learning (1989), Addison-Wesley: Addison-Wesley Reading, MA · Zbl 0721.68056
[59] Michalewicz, Z., Genetic Algorithms+Data Structures=Evolution Programs (1996), Springer: Springer Berlin · Zbl 0841.68047
[60] Koza, J. R., Genetic Programming: On the Programming of Computers by Means of Natural Selection (1992), MIT Press: MIT Press Cambridge, MA · Zbl 0850.68161
[61] Machado, J. T., What a fractional world!, Fract. Calc. Appl. Anal., 14, 4, 635-654 (2011) · Zbl 1273.37002
[63] Machado, J. T.; Costa, A. C.; Quelhas, M. D., On the DNA of eleven mammals, Int. J. Bifurcation Chaos, 22, 4, 1250074 (2012)
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