GC-content, the ratio of guanine and cytosine bases in an entire nucleotide sequence, and palindromic sequences are unique for every organism due to genomic evolution. The goals of our research was to establish a correlation between GC-content and palindromic densities in wild-type viral and randomly-generated genomes. Forty viral genomes were downloaded from GenBank and their GC-ratios and palindromic densities were calculated and plotted using Mathematica. The palindromic densities-by-GC-ratios plot of randomly generated sequences (palindromic density curve) exhibited a quadratic relationship and was superimposed over the viral genome plot. It was observed that the viral plots followed the curvature of the random sequences' quadratic curve, signifying a directly proportional relationship between GC-content and palindrome density in viral genomes. However, because viral genomes require certain non-palindromic sequences to function, the palindromic densities of most wild-type genomes were under the palindromic density curve. The variance in palindrome densities of wild-type genomes in respect to the random sequences' quadratic curve may be examined to determine evolutionary traits in genomes. A better understanding of viral palindromic densities and GC-ratios would help in understanding conserved secondary RNA structures in viral genomes and future drug discovery. In addition, certain viral genomes were found to be viable recombinant viruses, which are used in gene therapy.
BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes
Combining detection and reconstruction of correlational and quasi-periodic motifs in viral genomic sequences with transitional genome mapping: Application to COVID-19
基因组自身的过渡自同构映射（Transitional Automorphic Mapping of the Genome on Itself，TAMGI）方法旨在结合病毒基因组RNA/DNA序列中相关和准周期模体的检测和重建。通过TAMGI重建的基序对于插入缺失和点突变是稳健的，并且可以尝试作为推定的治疗靶标。我们开发并测试了相关的理论和统计标准的TAMGI应用程序。TAMGI的应用通过研究包装在类似病毒的螺旋衣壳中的严重急性呼吸道综合征冠状病毒SARS-CoV和SARS-CoV-2（后者的冠状病毒SARS-CoV-2负责COVID-19大流行）的基因组中的基序来说明。这样的核糖核衣壳被转运到球形膜被膜与掺入刺突糖蛋白。另外两个例子涉及二十面体衣壳病毒的基因组，卫星烟草花叶病毒（STMV）和噬菌体PHIX 174。这些病毒基因组中的部分准周期基序是由于基因组ssRNA/ssDNA与核衣壳蛋白之间的弱特异性合作相互作用而进化的。衣壳的对称性导致相关基因组序列中特定准周期基序的自然选择。一般来说，TAMGI为研究许多分子机制提供了一个方便的工具，这些机制涉及准周期基序和完整重复序列、基因组组织、顺式/反式调节元件的背景分析、数据挖掘以及基因组序列中的相关性。
An Investigation of Hepatitis B Virus Genome using Markov Models
Faculty of Engineering and IT, University of Technology Sydney（悉尼科技大学工程与信息技术学院）；Isfahan University of Technology（伊斯法罕理工大学）；Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University（迪肯大学智能系统研究与创新研究所）；Rutgers University（罗格斯大学）；Center for Computational and Integrative Biology, Rutgers University（罗格斯大学计算与整合生物学中心）
