A comprehensive computational model of facilitated diffusion in prokaryotes

<jats:title>Abstract</jats:title> <jats:p>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.</jats:p> <jats:p>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.</jats:p> <jats:p>Contact:  n.r.zabet@gen.cam.ac.uk</jats:p> <jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>