基于位置加权k-mer方法的HIV-1基因组系统发育分析
Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method.
作者信息
Ma Yuanlin, Yu Zuguo, Tang Runbin, Xie Xianhua, Han Guosheng, Anh Vo V
机构信息
Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China.
School of Economics, Zhengzhou University of Aeronautics, Zhengzhou 450046, China.
出版信息
Entropy (Basel). 2020 Feb 23;22(2):255. doi: 10.3390/e22020255.
HIV-1 viruses, which are predominant in the family of HIV viruses, have strong pathogenicity and infectivity. They can evolve into many different variants in a very short time. In this study, we propose a new and effective alignment-free method for the phylogenetic analysis of HIV-1 viruses using complete genome sequences. Our method combines the position distribution information and the counts of the -mers together. We also propose a metric to determine the optimal value. We name our method the () method. Validation and comparison with the Robinson-Foulds distance method and the modified bootstrap method on a benchmark dataset show that our method is reliable for the phylogenetic analysis of HIV-1 viruses. can resolve within-group variations for different known subtypes of Group M of HIV-1 viruses. This method is simple and computationally fast for whole genome phylogenetic analysis.
HIV-1病毒是HIV病毒家族中的主要类型，具有很强的致病性和传染性。它们能在极短时间内演变成许多不同的变体。在本研究中，我们提出了一种新的、有效的无比对方法，用于使用完整基因组序列对HIV-1病毒进行系统发育分析。我们的方法将位置分布信息和k-mer的计数结合在一起。我们还提出了一种度量标准来确定最优的k值。我们将我们的方法命名为k-PDP方法。在一个基准数据集上与罗宾逊-福尔兹距离法和改进的自展法进行验证和比较表明，我们的方法对于HIV-1病毒的系统发育分析是可靠的。k-PDP方法可以解析HIV-1病毒M组不同已知亚型的组内变异。该方法对于全基因组系统发育分析来说简单且计算速度快。
Zotero 插件