Computational Methods to Study Kinetics of DNA Replication
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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.