Geometrical Study of Virus RNA Sequences

Abstract

In this contribution, some applications of the earlier developed fast algorithm of calculating coordinates of single nucleotides and RNA fragments are considered to create multi-scale geometrical models of RNAs and their mutations. The algorithm allows to plot single nucleotides and RNA fragments on one figure and to track the RNA mutations of any level visually and numerically using interpolation formulas and point-to-point estimates of coordinates of ATG starting triplets and single nucleotides. The performed study of many samples of SARS CoV-2 viruses shows perturbations of ATG starting triplet coordinates in the vicinity of orf1ab gene end only.

Visual and Quantitative Analyses of Virus Genomic Sequences using a Metric-based Algorithm

“…Our approach supposes choosing a reference nucleotide sequence to compare the genomic virus data of other samples, and it is a complete genomic sequence MN988668.1 from GenBank (row 1, Table 1). Several virus samples from GenBank and GISAID have been studied in this way [42], and some results of comparisons are given in Fig. 7.…”

“…In many cases, the RNAs/DNAs have repeated patterns of nucleotide sequences, and these regions are better conserved in mutations [9]. Systems of these repeating fragments are considered as skeletons or schemes of these chains [41],[42]. As a rule, pattern discovery relates to nondeterministic polynomial time problems (NP-problems), i.e.…”

“…In some studied samples (here, and in Refs. [42], [68]), perturbations are near the end of the orf1ab gene, as is seen using a graphical tool of GenBank [39]. Perturbations were detected by calculating the i x coordinates according to known i y .…”

“…7 and Refs. [42], [68]). The origin of this is unknown, but it was not coupled with the lineages of viruses and their clades.…”