Yang Scott Cheng-Hsin, Gauthier Michel G, Bechhoefer John
Department of Physics, Simon Fraser University, Burnaby, BC, Canada.
Methods Mol Biol. 2009;521:555-73. doi: 10.1007/978-1-60327-815-7_32.
New technologies such as DNA combing have led to the availability of large quantities of data that describe the state of DNA while undergoing replication in S phase. In this chapter, we describe methods used to extract various parameters of replication--fork velocity, origin initiation rate, fork density, numbers of potential and utilized origins--from such data. We first present a version of the technique that applies to "ideal" data. We then show how to deal with, a number of real-world complications, such as the asynchrony of starting times of a population of cells, the finite length of fragments used in the analysis, and the finite amount of DNA in a chromosome.
诸如DNA梳理等新技术已使得大量描述DNA在S期复制时状态的数据得以获取。在本章中，我们描述了用于从此类数据中提取复制的各种参数的方法——复制叉速度、起始点起始速率、叉密度、潜在起始点和已利用起始点的数量。我们首先介绍适用于“理想”数据的技术版本。然后我们展示如何处理一些实际中的复杂情况，比如一群细胞起始时间的不同步性、分析中使用的片段的有限长度以及染色体中DNA的有限量。
