Rzhetsky A, Dopazo J, Snyder E, Dangler C A, Ayala F J
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA.
Genetics. 1996 Dec;144(4):1975-83. doi: 10.1093/genetics/144.4.1975.
We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partially digested with RNAse A, and the digestion products are compared on an electrophoretic gel. Here we provide an algorithm for converting the numbers of unique and matching electrophoretic bands into an estimate of the number of nucleotide differences between the sequences. Computer simulation indicates that the proposed method yields a robust estimate of the genetic distance despite stochastic errors and occasional violation of certain assumptions. Our study suggests that the method performs best when the distance between the sequences is < 15 differences. When the sequences under analysis are likely to have larger distances, we advise to substitute one long riboprobe with a set of shorter nonoverlapping probes. The new algorithm is applied to infer the proximity of several strains of pseudorabies virus.
我们提出了一种简单的算法，通过比较RNA或DNA序列对的核糖核酸酶A错配切割模式来估计它们之间的核苷酸差异数量。在核糖核酸酶A错配切割技术中，将两个或更多的样品序列与同一RNA探针杂交，用核糖核酸酶A对杂交体进行部分消化，并在电泳凝胶上比较消化产物。在此，我们提供一种算法，用于将独特和匹配的电泳条带数量转换为序列之间核苷酸差异数量的估计值。计算机模拟表明，尽管存在随机误差和偶尔违反某些假设的情况，但所提出的方法仍能可靠地估计遗传距离。我们的研究表明，当序列之间的距离小于15个差异时，该方法效果最佳。当所分析的序列可能有更大的距离时，我们建议用一组较短的非重叠探针替代一个长的核糖探针。新算法被应用于推断几种伪狂犬病病毒株的亲缘关系。
