Codon distributions in DNA

A. Som; S. Chattopadhyay; J. Chakrabarti; D. Bandyopadhyay

doi:10.1103/PhysRevE.63.051908

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Codon distributions in DNA

A. Som^1,*, S. Chattopadhyay^1,†, J. Chakrabarti^1,‡, and D. Bandyopadhyay^2,§

¹Department of Theoretical Physics, Indian Association for the Cultivation of Science, Calcutta 700 032, India
²Linguistics Research Unit, Indian Statistical Institute, Calcutta 700 035, India

^*Email address: tpas@mahendra.iacs.res.in
^†Email address: tpsc@mahendra.iacs.res.in
^‡Email address: tpjc@mahendra.iacs.res.in
^§Email address: bandyo@isical.ac.in

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Phys. Rev. E 63, 051908 – Published 18 April, 2001

DOI: https://doi.org/10.1103/PhysRevE.63.051908

Abstract

The codons, 64 in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency versus rank of the codons. These distributions are characterized by parameters that are almost universal, i.e., gene independent. There is but a small part that depends on the gene. We present the theory to calculate the universal (gene-independent) part. The part that is gene-specific, however, has undetermined overlaps and fluctuations.

References (13)

R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons, and H. E. Stanley, Phys. Rev. Lett. 73, 3169 (1994).
D. Welsh, Codes and Cryptography (Oxford University Press, Oxford, 1988).
E. W. Montroll and M. F. Shlesinger, in Nonequilibrium Phenomena II From Stochastics to Hydrodynamics, edited by J. L. Lebowitz and E. W. Montroll (North-Holland, Amsterdam, 1984).
G. K. Zipf, Human Behavior and the Principle of Least Effort (Addison-Wesly Press, Cambridge, MA, 1949).
R. F. Voss, Phys. Rev. Lett. 68, 3805 (1992); W. Li and K. Kaneko, Europhys. Lett. 17, 655 (1992); C.-K. Peng, S. V. Buldyrev, S. Havlin, M. Simons, H. E. Stanley, and A. L. Goldberger, Nature (London) 365, 168 (1992).
S. Karlin and V. Brendel, Science 259, 677 (1993); D. Larhammar and C. A. Chatzidimitriou-Dreissman, Nucl. Acid Res. 21, 5167 (1993); S. Nee, Nature (London) 357, 450 (1992).
A. Czirok, R. N. Mantegna, S. Havlin, and H. E. Stanley, Phys. Rev. E 52, 446 (1995).
B. Mandelbrot, Structures of Language, edited by R. Jacobson (AMS, New York, 1961); N. E. Israeloff, M. Kagalenko, and K. Chan, Phys. Rev. Lett. 76, 1976 (1996); ibid.R. F. Voss, 76, 1978 (1996); ibid.S. Bonhoeffer, A. V. M. Herz, Maarten C. Boerlijst, S. Nee, M. A. Nowak, and R. M. May, 76, 1977 (1996).
I. Kanter and D. A. Kessler, Phys. Rev. Lett. 74, 4559 (1995).
See S. Bonhoeffer et al., in Structures of Language (Ref. [8]).
A. A. Tsonis, J. B. Elsner, and P. A. Tsonis, J. Theor. Biol. 76, 25 (1997).
URL for EMBL database: http://www.embl-heidelberg.de/
URL for GenBank database: http://www.ncbi.nlm.nih.gov/Entrez/

[c1] R. N. Mantegna, S. V. Buldyrev, A. L. Goldberger, S. Havlin, C.-K. Peng, M. Simons, and H. E. Stanley, Phys. Rev. Lett. 73, 3169 (1994).

[c2] D. Welsh, Codes and Cryptography (Oxford University Press, Oxford, 1988).

[c3] E. W. Montroll and M. F. Shlesinger, in Nonequilibrium Phenomena II From Stochastics to Hydrodynamics, edited by J. L. Lebowitz and E. W. Montroll (North-Holland, Amsterdam, 1984).

[c4] G. K. Zipf, Human Behavior and the Principle of Least Effort (Addison-Wesly Press, Cambridge, MA, 1949).

[c5] R. F. Voss, Phys. Rev. Lett. 68, 3805 (1992); W. Li and K. Kaneko, Europhys. Lett. 17, 655 (1992); C.-K. Peng, S. V. Buldyrev, S. Havlin, M. Simons, H. E. Stanley, and A. L. Goldberger, Nature (London) 365, 168 (1992).

[c6] S. Karlin and V. Brendel, Science 259, 677 (1993); D. Larhammar and C. A. Chatzidimitriou-Dreissman, Nucl. Acid Res. 21, 5167 (1993); S. Nee, Nature (London) 357, 450 (1992).

[c7] A. Czirok, R. N. Mantegna, S. Havlin, and H. E. Stanley, Phys. Rev. E 52, 446 (1995).

[c8] B. Mandelbrot, Structures of Language, edited by R. Jacobson (AMS, New York, 1961); N. E. Israeloff, M. Kagalenko, and K. Chan, Phys. Rev. Lett. 76, 1976 (1996); ibid.R. F. Voss, 76, 1978 (1996); ibid.S. Bonhoeffer, A. V. M. Herz, Maarten C. Boerlijst, S. Nee, M. A. Nowak, and R. M. May, 76, 1977 (1996).

[c9] I. Kanter and D. A. Kessler, Phys. Rev. Lett. 74, 4559 (1995).

[c10] See S. Bonhoeffer et al., in Structures of Language (Ref. [8]).

[c11] A. A. Tsonis, J. B. Elsner, and P. A. Tsonis, J. Theor. Biol. 76, 25 (1997).

[c12] URL for EMBL database: http://www.embl-heidelberg.de/

[c13] URL for GenBank database: http://www.ncbi.nlm.nih.gov/Entrez/

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Codon distributions in DNA

Abstract

References (13)

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