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lüll Parsing regulatory DNA: general tasks, techniques, and the PhyloGibbs approach Siddharthan RJ Biosci 2007[Aug]; 32 (5): 863-70In 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.|*Sequence Analysis, DNA/methods[MESH]|*Software[MESH]|Animals[MESH]|Base Sequence[MESH]|Computational Biology/*methods[MESH]|DNA/chemistry/*genetics[MESH]|Humans[MESH]|Molecular Sequence Data[MESH]|Regulatory Elements, Transcriptional/*genetics[MESH]|Regulatory Sequences, Nucleic Acid/*genetics[MESH] |