Parsing regulatory DNA: General tasks, techniques, and the PhyloGibbs approach
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In this review, we discuss the general problem of understanding transcriptional regulation from DNA sequence and prior information. The main tasks we discuss are predicting local regions of DNA, cis-regulatory modules (CRMs) that contain binding sites for transcription factors (TFs), and predicting individual binding sites. We review various existing methods, and then describe the approach taken by PhyloGibbs, a recent motif-finding algorithm that we developed to predict TF binding sites, and PhyloGibbs-MP, an extension to PhyloGibbs that tackles other tasks in regulatory genomics, particularly prediction of CRMs.
KeywordsPhyloGibbs regulatory DNA transcription factors
Markor Chain Monte Corlo
position weight matrices
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