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A comprehensive computational model of facilitated diffusion in prokaryotes.

ABSTRACT: 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.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.

SUBMITTER: Zabet NR 

PROVIDER: S-EPMC3356843 | biostudies-other | 2012 Jun

REPOSITORIES: biostudies-other

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A comprehensive computational model of facilitated diffusion in prokaryotes.

Zabet Nicolae Radu NR   Adryan Boris B  

Bioinformatics (Oxford, England) 20120406 11

<h4>Motivation</h4>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.<h4>Results</h4>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 demonstra  ...[more]