DNA walks in virus genomics

Abstract

This paper studies published results in imaging and digital processing of virus RNAs (ribonucleic acid) using DNA (deoxyribonucleic acid) walks. The complicated nature and physicochemical properties of these nucleotide chains hinder the development of a universal method of numerical mapping and plotting of RNAs, and many algorithms that exist are reviewed here, including 2-D and 3-D DNA walks, walks in complex space, multi-dimensional dynamic representations of DNAs, etc. A detailed analysis in virus genomics is performed for a recently proposed query-walk algorithm and multi-level graphical representation of the traces of repeated patterns in RNA chains. They are represented by binary strings and compared with a sought query, calculating the Hamming distance in every comparison step. The coordinates of the found patterns or queries are defined, and a walk is composed of a set of consecutive numbers of these queries along the studied RNA. The primary attention of this review is paid to ATG triplets, which are starting nucleotides of codons (words) in most cases. As follows from the analyzed papers, the severe mutations of viruses touch the compactness of ATG curve sets of viruses and de-cluster the fractal dimension values of word-length distributions. The material of this review is helpful in the digital and visual studies of viruses.

DNA walks in virus genomics