These code are for training RBF neural networks to mapping the positions at DNA and its binding rate, which is described in detail in paper:
Modeling in vivo dynamics of RNA polymerase II meeting Nucleosomes Roozbeh Abedini-Nassab, Xu Zhang
Abstract: Nucleosomes are shown to be barriers for RNA Polymerase II elongation along DNA, and their entry site behaves as the major obstacle. In this work, based on recent available in vivo data, we introduce a mathematical model for RNA Polymerase II reads. Moreover, as an alternative way, we use Radial Basis Function Network to predict RNA Polymerase II reads. Results of our models are in good agreement with experimental data. Furthermore, we introduce a random walk model which includes stalling, backtracking, and elongation phenomena. This model can predict and simulate the RNA Polymerase II trajectory on DNA, when it meets various nucleosomes.
Paper link:
http://www.sciencepubco.com/index.php/ijet/article/view/6098