Izvestiya of Saratov University.

Physics

ISSN 1817-3020 (Print)
ISSN 2542-193X (Online)

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Ulyanov S. S., Ulianova O. V., Zaitsev S. S., Khizhnyakova M. A., Saltykov I. V., Filonova N. N., Subbotina I. A., Lyapina A. M., Feodorova V. A. Study of Statistical Characteristics of GB-speckles, Forming at Scattering of Light on Virtual Structures of Nucleotide Gene Sequences of Enterobacteria. Izvestiya of Saratov University. Physics , 2018, vol. 18, iss. 2, pp. 123-137. DOI: 10.18500/1817-3020-2018-18-2-123-137

This is an open access article distributed under the terms of Creative Commons Attribution 4.0 International License (CC-BY 4.0).
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Language: 
Russian
Heading: 
Biophysics and medical physics
UDC: 
535.41
DOI: 
10.18500/1817-3020-2018-18-2-123-137

Study of Statistical Characteristics of GB-speckles, Forming at Scattering of Light on Virtual Structures of Nucleotide Gene Sequences of Enterobacteria

Autors: 
Ulyanov Sergei Sergeevich, Saratov State University
Ulianova Onega Vladimirovna, Saratov Branch of Federal Research Center for Virology and Microbiology
Zaitsev Sergei Sergeevich, Saratov Branch of Federal Research Center for Virology and Microbiology
Khizhnyakova Mariia Aleksandrovna, Saratov Branch of Federal Research Center for Virology and Microbiology
Saltykov Iurii Vladimirovich, Saratov State Agrarian University named after N.I. Vavilov
Filonova Nadezhda Nikolaevna, Saratov Branch of Federal Research Center for Virology and Microbiology
Subbotina Irina Anatol'evna, Saratov Branch of Federal Research Center for Virology and Microbiology
Lyapina Anna Mikhailovna, Saratov Branch of Federal Research Center for Virology and Microbiology
Feodorova Valentina Anatol'evna, Saratov State University
Abstract: 

Background and Objectives: A brief review of methods of modern bioinformatics, based on the usage of virtual optical GBspeckles (gene-based speckles), has been presented in this paper. An algorithm of transformation of a nucleotide sequence into a 2D GB-speckle-structure has been proposed and discussed. Materials and Methods: Computer simulation of the process of formation of GB-speckles at the scattering of coherent light on quasi-random virtual surfaces, corresponding to initial nuclear sequence of the genes, encoded by the Omptin family proteins, such as SopA, OmpP, OmpT, PgtE and Pla in Enterobacteriaceae spp. has been carried out. Results: Statistical properties of GB-speckles, coding of different sequences of the genes have been investigated. Conclusion: It has been shown that GB-speckles of this type obey Gaussian statistics. It has also been found that classical methods of statistical analysis of GB speckles are not informative and low-effective from a viewpoint of detection of common fragments in initial nucleotide sequences. However, a direct comparison of the probability density functions of spatial fluctuations of the speckle intensity allows to find common motifs of the comparing genes. A criterion for the reliable detection of the presence of common motifs in these genes, based on the methods of speckle-optics has been suggested. These motifs could be innovated promising molecular targets for the development of a new generation of effective synthetic Omptin-based peptide precise medical devices for smart laboratory diagnostics of a group of Gramnegative Enterobacterial pathogens.

Key words: 
nucleotide sequence
GB speckles
reference sequence
diffraction of coherent light
SNP
virtual random surfaces
Omptin proteins
gene
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