Clough J E, Foster J A, Barnett M, Wichman H A
Department of Computer Science, University of Idaho, Moscow 83844-1010, USA.
J Mol Evol. 1996 Jan;42(1):52-8. doi: 10.1007/BF00163211.
It has been proposed that the most extensively studied mammalian retrotransposons replicate by some form of a master template model. This conclusion has been drawn largely from DNA sequence analysis and is based on phylogenetic tree topology, the presence and ordering of shared variants, the degree of divergence between elements within a subfamily, and the shape of the distribution of pairwise differences between elements. To investigate how robust these parameters are as predictors of the model of transposition, computer simulations of the two most extreme transposition models, the Random Template Model and the Strict Master Model, were carried out. A prototype of a computer simulator for studying retrotransposition is presented. The simulator is a versatile digital workbench that maintains DNA sequence data and allows manipulation of a range of factors including reverse transcriptase and in situ mutation rates, transposition template, and transposition rate. All parameters previously used as predictors of the model of transposition were markedly different for the two extreme models when evaluated using large sample sizes of sequences from experiments simulating up to 15 million years of evolution.
有人提出，研究最为广泛的哺乳动物逆转录转座子通过某种形式的主模板模型进行复制。这一结论主要是通过DNA序列分析得出的，基于系统发育树拓扑结构、共享变异的存在与排序、亚科内元件之间的差异程度以及元件之间成对差异分布的形状。为了研究这些参数作为转座模型预测指标的可靠性，对两种最极端的转座模型——随机模板模型和严格主模型进行了计算机模拟。本文展示了一个用于研究逆转录转座的计算机模拟器原型。该模拟器是一个多功能数字工作台，可维护DNA序列数据，并允许对一系列因素进行操作，包括逆转录酶和原位突变率、转座模板和转座率。当使用模拟长达1500万年进化的实验中大量的序列样本进行评估时，先前用作转座模型预测指标的所有参数在两种极端模型中都有显著差异。
