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A schematic view of the integrated framework. A single motif, denoted by mg, consists of two parts, mg is how well the sequence matches a consensus, while og is a prior on whether any regulatory element is to occur at that position. A set of single motifs, together with inter-motif distance restrictions (d), then forms a composite motif (cg). Finally, multiple occurrences of a composite motif in the regulatory regions of a gene is represented by a gene score Gc.
