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We present a calculation technique for modeling inhomogeneous DNA replicationkinetics, where replication factors such as initiation rates or fork speeds canchange with both position and time. We can use our model to simulate data setsobtained by molecular combing, a widely used experimental technique for probingreplication. We can also infer information about the replication program byfitting our model to experimental data sets and also test the efficacy ofplanned experiments by fitting our model to simulated data sets. We considerasynchronous data sets and illustrate how a lack of synchrony affectsreplication profiles. In addition to combing data, our technique iswell-adapted to microarray-based studies of replication.

Numerical modeling of inhomogeneous DNA replication kinetics