Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, IL 60607, USA.
Department of Biological Sciences, Chicago State University, IL 60628, USA.
J Theor Biol. 2014 May 7;348:12-20. doi: 10.1016/j.jtbi.2014.01.022. Epub 2014 Jan 29.
In this paper, we develop a novel method to study the viral genome phylogeny. We apply Lempel-Ziv complexity to define the distance between two nucleic acid sequences. Then, based on this distance we use the Hausdorff distance (HD) and a modified Hausdorff distance (MHD) to make the phylogenetic analysis for multi-segmented viral genomes. The results show the MHD can provide more accurate phylogenetic relationship. Our method can have global comparison of all multi-segmented genomes simultaneously, that is, we treat the multi-segmented viral genome as an entirety to make the comparative analysis. Our method is not affected by the number or order of segments, and each segment can make contribution for the phylogeny of whole genomes. We have analyzed several groups of real multi-segmented genomes from different viral families. The results show that our method will provide a new powerful tool for studying the classification of viral genomes and their phylogenetic relationships.
在本文中，我们开发了一种新的方法来研究病毒基因组系统发育。我们应用 Lempel-Ziv 复杂度来定义两个核酸序列之间的距离。然后，基于这个距离，我们使用 Hausdorff 距离（HD）和改进的 Hausdorff 距离（MHD）对多分段病毒基因组进行系统发育分析。结果表明，MHD 可以提供更准确的系统发育关系。我们的方法可以同时对所有多分段基因组进行全局比较，即我们将多分段病毒基因组作为一个整体进行比较分析。我们的方法不受片段数量或顺序的影响，每个片段都可以为整个基因组的系统发育做出贡献。我们已经分析了来自不同病毒科的几组真实的多分段基因组。结果表明，我们的方法将为研究病毒基因组的分类和系统发育关系提供一种新的强大工具。
