Issue August 2000

category image Volume 18
No. 1 (p 1-168)
August 2000
ISSN 0739-1102

Basic Properties of Populations Generated in the Frame of One-Parameter Discrete Model of Genetic Diversity (p. 103-112)

Previously, when discussing the properties of one parameter discrete model of genetic diversity (M. Yu. Shchelkanov et al., J. Biomol. Struct. Dyn. 15, 887-894 (1998)), we took into account Hamming distance distribution only between precursor and arbitrary descendant sequences. However, really there are sets of sequence populations produced during amplification process. In the presented work we have investigated Hamming distance distributions between sequences from different descendant sets produced in the frame of one parameter discrete model. Two basic descendant generation operators (so called amplifiers) are introduced: i) the last generation amplifier, L, which produces descendants with precursor elimination; ii) all generations amplifier, G, which produces descendants without precursor elimination. Generalization of one-parameter discrete model for the case when precursor sequences do not coincide are carried out. Using this generalization we investigate the distribution of Hamming distances between L - and G -generated sequences. Basic properties of L and G operators, L / G -choice alternative problem have been discussed. Obtained results have common theoretical significance, but they are more suitable for high level genetic diversity process (for example, HIV diversity).

Michael Yu. Shchelkanov1,2,3*
Lev A. Soinov2
Maxim S. Petrenko2
Nicole S. Starikov2
Vadim V. Zalunin4
Alexander A. Slavsky1,2
Maxim V. Denisov2
Victor B. Kireev2
Andrey Yu. Surovoy3

1D. I. Ivanovsky Institute of Virology
RAMS, Gamaley str., 16
Moscow, 123098 Russia
2Moscow Institute of Physics and Technology
Faculty of Physicochemical Biology
Department of Molecular Biophysics
Dolgoprudny, Moscow region
141700 Russia
3M. M. Shemyakin and Yu. A. Ovchinnikov
Institute of Bioorganic Chemistry
Laboratory of Peptide Chemistry
Miklukho-Maklay 16/10
Moscow, 117871 Russia
4Los Alamos National Laboratory
Theoretical Biology and Biophysics Group
Los Alamos, NM, USA
*adorob@hotmail.com

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