In silico framework for genome analysis

Genomes hold the complete genetic information of an organism. Examining and analyzing genomic data plays a critical role in properly understanding an organism, particularly the main characteristics, functionalities, and evolving nature of harmful viruses. However, the rapid increase in genomic data poses new challenges and demands for extracting meaningful and valuable insights from large and complex genomic datasets. In this paper, a novel Framework for Genome Data Analysis (F4GDA), is developed that offers various methods for the analysis of viral genomic data in various forms. The framework’s methods can not only analyze the changes in genomes but also various genome contents. As a case study, the genomes of five SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) VoC (variants of concern), which are divided into three types/groups on the basis of geographical locations, are analyzed using this framework to investigate (1) the nucleotides, amino acids and synonymous codon changes in the whole genomes of VoC as well as in the Spike (S) protein, (2) whether different environments affect the rate of changes in genomes, (3) the variations in nucleotide bases, amino acids, and codon base compositions in VoC genomes, and (4) to compare VoC genomes with the reference genome sequence of SARS-CoV-2.