Sengupta Dipendra C, Hill Matthew D, Benton Kevin R, Banerjee Hirendra N
Department of Mathematics, Computer Science & Engineering Technology, Elizabeth City State University, Elizabeth City, North Carolina, USA.
Department Natural Sciences, Elizabeth City State University, Elizabeth City, North Carolina, USA.
Comput Mol Biosci. 2020 Sep;10(3):61-72. doi: 10.4236/cmb.2020.103004.
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.
新型冠状病毒（SARS-COV-2）通常被称为新冠病毒，已传播至213个国家，确诊病例近700万，死亡近40万。如此大规模的疫情爆发需要对病毒基因组序列进行分类和溯源，以进行规划、防控和治疗。出于上述需求，我们报告了两种与混沌游戏表示法（CGR）相结合的无比对方法，用于进行聚类分析并据此创建系统发育树。对于每个DNA序列，我们关联一个矩阵，然后将两个DNA序列之间的距离定义为它们相关矩阵之间的距离。这些方法正用于冠状病毒序列的系统发育分析。我们的方法为分析和注释基因组及其系统发育关系提供了一个强大的工具。我们还将我们的工具与最流行的比对方法之一ClustalX算法进行了比较。结果表明，我们的无比对方法能够找到冠状病毒最亲近的基因亲属。
