  We present a calculation technique for modeling inhomogeneous DNA replication
kinetics, where replication factors such as initiation rates or fork speeds can
change with both position and time. We can use our model to simulate data sets
obtained by molecular combing, a widely used experimental technique for probing
replication. We can also infer information about the replication program by
fitting our model to experimental data sets and also test the efficacy of
planned experiments by fitting our model to simulated data sets. We consider
asynchronous data sets and illustrate how a lack of synchrony affects
replication profiles. In addition to combing data, our technique is
well-adapted to microarray-based studies of replication.
