TITLE:
Evolutionary Relationship of Protein Sequences of SARS-CoV-2 and Other Viruses through Chaos Game Representation
AUTHORS:
Matthew D. Hill, Kevin E. Simmons, Dipendra C. Sengupta
KEYWORDS:
Chaos Game Representation (CGR), Protein, Multi-Dimensional Scaling (MDS)
JOURNAL NAME:
Computational Molecular Bioscience,
Vol.12 No.3,
September
30,
2022
ABSTRACT: Comparison between different biological sequences is a key step in bioinformatics when analyzing similarities of sequences and phylogenetic relationships. A method of graphically representing biological sequences known as Chaos Game Representation (CGR) has achieved many applications in the studies of bioinformatics. The key issue in the application of CGR is to extract as many useful features as possible from CGR. Initially, CGR was applied to DNA sequences, but in this paper, a CGR-based approach is used to extract suitable features for comparing protein sequences of SARS-CoV-2 and other viruses. For this aim, several viral protein sequences from 12 groups are considered and CGR centroid, amino acid frequency, compounded frequency, Shannon entropy, and Kullback-Lieber Discrimination Information are applied to find the inter-relationship among the sequences. The experimental results demonstrate the potential strengths of CGR-based method for examining the evolutionary relationship of protein sequences. Our method is powerful for extracting effective features from protein sequences, and therefore important in classifying proteins and inferring the phylogeny of viruses.