Computational Methods to Study Kinetics of DNA Replication

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.