Abstract
The novel coronavirus (SARS-COV-2) is generally referred to as Covid-19 virus has spread to 213 countries with nearly 7 million confirmed cases and nearly 400,000 deaths. Such major outbreaks demand classification and origin of the virus genomic sequence, for planning, containment, and treatment. Motivated by the above need, we report two alignment-free methods combing with CGR to perform clustering analysis and create a phylogenetic tree based on it. To each DNA sequence we associate a matrix then define distance between two DNA sequences to be the distance between their associated matrix. These methods are being used for phylogenetic analysis of coronavirus sequences. Our approach provides a powerful tool for analyzing and annotating genomes and their phylogenetic relationships. We also compare our tool to ClustalX algorithm which is one of the most popular alignment methods. Our alignment-free methods are shown to be capable of finding closest genetic relatives of coronaviruses.
Highlights
Deoxyribonucleic Acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms
We proposed two methods, i.e., probability matrix method and centroid matrix method combining with Chaos Game Representation (CGR) to construct distancematrix between two genomes, and create dendrogram using Hierarchical Agglomerative Clustering (HAC) analysis
A CGR associates an image to each DNA sequence as follows: starting from a square with corner labeled four nucleotides C, G, A and T, and the center of the square as the starting point, the image is obtained by successively plotting nucleotide as the middle point between the current point and the corner labeled by the nucleotide to be plotted
Summary
One of the goals of this study was to identify what distance is better able to differentiate the structural differences of various genomic DNA sequences
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