Polarization Analysis of Gene Sequence Structures: Mapping of Extreme Local Polarization States

Abstract

A method for visualization and identification of nucleotide sequences is proposed based on the synthesis of phase screens displaying the structure of the analyzed sequences and reconstruction of binary maps of the extreme values of the local Stokes vector components in the diffraction zone. This diffraction zone is formed due to reading out the phase screen by a coherent collimated beam with two orthogonally polarized (x–y) components. With different phase delays of the x–y components of the readout beam introduced by the phase screen elements, this causes a variety of local polarization states in the diffraction zone. The discrimination level for the local component of the Stokes vector chosen for the binary mapping is established near the extreme value for this component. Computer verification of the proposed method using nucleotide sequences for various strains of the model African swine fewer (ASF) virus as the test objects shows its high efficiency in the detection of differences between two compared sequences corresponding to the same type of infectious agent. Analysis of the model data for the strains under study made it possible to establish a power-law character of correlation coefficients of the synthesized binary distributions of extreme local polarization states depending on the discrimination threshold detuning from the maximum value of the Stokes vector component used for the mapping .