Cite this article as:

Ulianova О. V., Ulyanov S. S., Zaitsev S. S., Khizhnyakova М. А., Saltykov Y. V., Filonova N. N., Subbotina I. А., Lyapina А. М., Feodorova V. А. 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. New series. Series Physics, 2018, vol. 18, iss. 2, pp. 123-137. DOI: https://doi.org/10.18500/1817-3020-2018-18-2-123-137


UDC: 
535.41
Language: 
Russian

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

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.

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