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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >PROKARYOTE PHYLOGENY WITHOUT SEQUENCE ALIGNMENT: FROM AVOIDANCE SIGNATURE TO COMPOSITION DISTANCE
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PROKARYOTE PHYLOGENY WITHOUT SEQUENCE ALIGNMENT: FROM AVOIDANCE SIGNATURE TO COMPOSITION DISTANCE

机译：不进行序列对齐的原核生物系统发育：从避免签名到组成距离

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摘要

This is a review of a new and essentially simple method of inferring phylogenetic relationships from complete genome data without using sequence alignment. The method is based on counting the appearance frequency of oligopeptides of a fixed length (up to K=6) in the collection of protein sequences of a species. It is a method without fine adjustment and choice of genes. Applied to prokaryotic genomes it has led to results comparable with the bacteriologists' systematics as reflected in the latest 2002 outline of the Bergey's Manual of Systematic Bacteriology. The method has also been used to compare chloroplast genomes and to the phylogeny of Coronaviruses including human SARS-CoV. A key point in our approach is subtraction of a random background from the original counts by using a Markov model of order K-2 in order to highlight the shaping role of natural selection. The implications of the subtraction procedure is specially analyzed and further development of the new approach is indicated.
机译：这是对一种新的且实质上简单的方法的综述，该方法无需使用序列比对即可从完整的基因组数据推断系统发生关系。该方法基于对物种蛋白质序列集合中固定长度（最多K = 6）的寡肽的出现频率进行计数。这是一种无需精细调整和选择基因的方法。应用于原核生物基因组，其结果可与细菌学家的系统学相媲美，这反映在2002年Bergey的《系统细菌学手册》的最新大纲中。该方法也已用于比较叶绿体基因组和冠状病毒（包括人SARS-CoV）的系统发育。我们方法中的关键点是通过使用K-2阶马尔可夫模型从原始计数中减去随机背景，以突出自然选择的塑造作用。专门分析了减法程序的含义，并指出了新方法的进一步发展。

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