p-adic modelling of the genome and the genetic code

Computer Journal

Volumn 53, Issue 4, 2010, Pages 432-442

  Dragovich, Branko ^a   Dragovich, Alexandra ^b  

^a UNIVERSITY OF BELGRADE   (Serbia)

^b VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

Author keywords

Evolution of the genetic code; Genetic code; Genome; P adic genomic space; P adic modelling

Indexed keywords

AMINO ACIDS AND PROTEINS; COMPUTER PROGRAM; FOUR AMINO ACIDS; GENETIC CODE; GENOMIC INFORMATION; GENOMICS; INFORMATION SPACES; PRIME NUMBER; RNA SEQUENCES; SINGLE NUCLEOTIDES;

AMINO ACIDS; DNA SEQUENCES; INFORMATION SYSTEMS; NUCLEOTIDES; ORGANIC ACIDS; RNA;

GENES;

EID: 77951903812     PISSN: 00104620     EISSN: 14602067     Source Type: Journal    
DOI: 10.1093/comjnl/bxm083     Document Type: Article

References (29)

1. Watson, J. D., Baker, T. A., Bell, S. P., Gann, A., Levine, M. and Losick, R. (2004) Molecular Biology of the Gene. CSHL Press, Benjamin Cummings, San Francisco.
2. Finkelshtein, A. V. and Ptitsyn, O. B. (2002) Physics of Proteins. Academic Press, London.
3. Frappat, L., Sciarrino, A. and Sorba, P. (2001) Crystalizing the genetic code. J. Biol. Phys., 27, 1-38. arXiv:physics/0003037. (Pubitemid 32983175)
4. Hornos, J. E. M. and Hornos, Y. M. M. (1993) Algebraic model for the evolutionofthe genetic code. Phys. Rev. Lett., 71, 4401-4404.
5. Forger, M. and Sachse, S. (2000) Lie superalgebras and the multiplet structure of the genetic code I: codon representations. J. Math. Phys., 41, 5407-5422. arXiv:math-ph/9808001.
6. Bashford, J. D., Tsohantjis, I. and Jarvis, P. D. (1997) Codon and nucleotide assignments in a supersymmetric model of the genetic code. Phys. Lett. A, 233, 481-488.
7. Dragovich, B. and Dragovich, A. (2006) A p-adic model of DNA sequence and genetic code. arXiv:q-bio. GN/0607018v1. http://www.arxiv.org/abs/q-bio. GN/0607018v1.
8. Dragovich, B. and Dragovich, A. (2007) p-adic Degeneracy of the genetic code. SFIN A, 20, 179-188. arXiv:0707.0764v1 [q-bio. GN].
9. Khrennikov, A. and Kozyrev, S. (2007) Genetic code on the diadic plane. Physica A: Stat. Mech. Appl., 381, 265-272. arXiv:q-bio/0701007. (Pubitemid 46829658)
10. Khrennikov, A. (2006) Gene expression from polynomial dynamics in the 2-adic information space. arXiv:q-bio/0611068v2. http://www.arxiv.org/abs/q-bio. OT/0611068v2.
11. Brekke, L. and Freund, P. G. O. (1993) p-adic numbers in physics. Phys. Rept., 233, 1-66.
12. Vladimirov, V. S., Volovich, I. V. and Zelenov, E. I. (1994) p-Adic Analysis and Mathematical Physics. World Scientific, Singapore.
13. Dragovich, B. (2004) p-adic and adelic quantum mechanics. Proc. V. A. Steklov Inst. Math., 245, 72-85. arXiv:hep-th/0312046.
14. Dragovich, B. (2006) p-adic and adelic cosmology: p-adic origin of dark energy and dark matter. p-adic mathematical physics. AIP Conf. Proc., 826, 25-42. arXiv:hep-th/0602044.
15. Avetisov, V. A., Bikulov, A. Kh., Kozyrev, S. V. and Osipov, V. A. (2002) p-adic models of ultrametric diffusion constrained by hierarchical energy landscape. J. Phys. A: Math. Gen., 35, 177-189. arXiv:cond-mat/0106506.
16. Khrennikov, A. (2004) Information Dynamics in Cognitive, Psychological, Social and Anomalous Phenomena. Kluwer AP, Dordrecht.
17. (2006) p-Adic Mathematical Physics, Proceedings of the 2nd International Conference on p-Adic Mathematical Physics, Belgrade, Serbia and Montenegro, 15-21 September 2005. In Khrennikov, A. Yu, Rakic, Z. and Volovich, I. V. (eds). AIP Conf. Proc., 826.
18. Gouvêa, F. Q. (1993) p-Adic numbers: An introduction (Universitext). Springer, Berlin.
19. Wikipedia, (2007) Amino acid. http://en. wikipedia.org/wiki/Amino-acid.
20. Jukes, T. H. (1983) Evolution of the amino acid code: inferences from mitochondrial codes. J. Mol. Evol., 19, 219-225.
21. Wikipedia, (2007) List of standard amino acids. http://en. wikipedia.org/wiki/List-of-standard-amino-acids.
22. Trifonov, E. N. (2004) The triplet code from first principles. J. Biomol. Struct. Dyn., 22, 1-11.
23. Crick, F. (1968) The origin of the genetic code. J. Mol. Biol., 38, 367-379.
24. Rumer, Yu. B. (1966) On systematization of codons in the genetic code. Doklady Acad. Nauk USSR, 167, 1393-1394.
25. Swanson, R. (1984) A unifying concept for the amino acid code. Bull. Math. Biol., 46, 187-203.
26. Hayes, B. (1998) The invention of the genetic code. Am. Sci., 86, 8-14. (Pubitemid 128500300)
27. Knight, R. D., Freeland, S. J. and Landweber, L. F. (2001) Rewiring the keyboard: evolvability of the genetic code. Nat. Rev. Genet., 2, 49-58.
28. Osawa, S., Jukes, T. H., Watanabe, K. and Muto, A. (1992) Recent evidence for evolution of the genetic code. Microb. Rev., 56, 229-264.
29. Wong, J. T. F. (1975) A co-evolution theory of the genetic code. Proc. Nat. Acad. Sci. USA, 72, 1909-1912.