A comprehensive computational model of facilitated diffusion in prokaryotes

Motivation: Gene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed. Results: We present a comprehensive computational model of the search process of TF for their genomic target site(s). The computational model considers: the DNA sequence, various TF species and the interaction of the individual molecules with the DNA or between themselves. We also demonstrate a systematic approach how to parametrize the system using available experimental data. Contact: n.r.zabet@gen.cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.