Similarity Studies of Corona Viruses through Chaos Game Representation

• 作者: Dipendra C. Sengupta Hirendra N. Banerjee Kevin R. Benton Matthew D. Hill
• 来源期刊: 计算分子生物学(英文)
• 学科: 医学
• 关键词: Covid-19 Chaos Game Representation Deoxyribonucleic Acid Phylogenetic Analysis Shannon Entropy
• 年，卷（期）: 2020,（3）
• 页码范围: 61-72
• 页数: 12页
• 分类号: R37

摘要

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.