Set-Theoretical Data Models in the Problem of Calculating Secondary Structures of RNA

Abstract

The tasks of counting the secondary structures of nucleotide sequences are a special case of combinatorial problems of high complexity (NP-problems) that can be solved by logic-heuristic methods. In addition, it is possible to use special software programs to solve the calculation of secondary structures of RNA nucleotide sequences for phylogenetic analysis (recovery of all mutations from an ancestor to the next one). In this paper, we propose more general means of data presentation and more powerful algorithms for calculating the secondary structures of RNA nucleotide sequences than in previous works of the author. In addition, we note that the software has great flexibility to solve problems of phylogenetic analysis. Computational experiments, the results of which are presented in this work, were carried out on the primary data taken from the website www.ncbi.nlm.nih.gov. In addition, data were also taken from the GenBank (USA) and EMBL (Europe) nucleotide sequence banks. The adaptation of the developed methods for calculating secondary structures was first carried out by searching for the full range of perfect repeats in genetic texts (the genomes of Bradyrhizobium japonicum (BA0000040_GR), Streptomyces avermitilis (BA0000030_GR)). As a result, a program was created that is customizable in many ways, including working in the alphabet, with extended consensus symbols (for more details, see the introduction).