Chromatic Differentiation of Functional Mappings of the Composition of Nucleic Acids

Abstract

Color visualization of the DNA of diverse living beings can help in the exploration of the issue of chromatic differentiation of functional mappings of the nucleotide composition of DNA molecules. By “chromatic differentiation”, we mean the coloring of these mappings. Algorithms for coloring genetic representations improve the perception of complex genetic information using color. Methodologically, to build the chromatic differentiation of functional mappings of the nucleotide composition of DNA, we employed the system of nucleotide Walsh functions and the Chaos Game Representation (CGR) algorithm. The authors compared these two approaches and proposed a modified CGR algorithm. The work presents various algorithms of chromatic differentiation based on the nucleotide Walsh functions at a specific location of the fragment in the nucleotide chain and on the frequencies of those fragments. The results of the analysis provide examples of chromatic differentiation in a variety of parametric spaces. The paper describes various approaches to coloring and video animation of DNA molecules in their chromatically differentiated spans of physicochemical parameters.

Visualization of the Signals Entropy Structure Based on Walsh–Hadamard Functions

“…Many bacteria and microorganisms, in particular, have unique genetic patterns that are extraordinarily diverse and can now be visualized using new imaging methods. These algorithms have already contributed significantly to science by enabling researchers to visualize the structure of DNA [1][2][3].…”

“…These studies are of interest from the perspectives of dynamic chaos theory, phase attractors theory, programming theory, and information processing theory. Before describing the experiments and their results, let us review the critical provisions outlined in our previous articles [1][2][3].…”

“…Each nucleotide is encoded using physicochemical parameters (subalphabets) such as purine/pyrimidine, keto/amino, and 2 or 3 hydrogen bonds. In other words, after choosing the method for setting the coding matrix (in this article, we only deal with the Hadamard nucleotide matrix, which is used in molecular genetic algorithms [1][2][3]), the basic algorithm consists of three main stages: scaling (choosing the scale parameter N); cutting the sequence into equal parts across all sub-alphabets; and building a visual representation in a particular geometric space. There are various options for structural mapping spaces, as discussed in our previous articles [1][2][3].…”

“…In this article, we will address methodological issues regarding the study of various noises and signals using new methods obtained from biophysical research [1][2][3]. To compare chaotic and quasi-chaotic signals, we will use various generators of pseudo-random numbers ("bad" noise generators) and examine various sources of natural noise.…”

“…To conduct our research, we will use visualization methods we have previously developed [1][2][3], based on the principles of matrix analysis of the molecular genetic structure of Symmetry 2024, 16, 59 2 of 14 DNA and RNA molecules. Our visualization methods allow us to display the structure of nucleic acids in different parametric spaces with different dimensions and coordinate systems.…”