MotifSampler tries to find over-represented motifs in the upstream region of a set of co-regulated genes. This motif finding algorithm uses Gibbs sampling to find the position probability matrix that represents the motif. In this implementation we focus on the use of higher-order background models to improve the robustness of the motif finding. At the moment the MotifSampler comes with background models for several organisms .
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Thijs G., Lescot M., Marchal K., Rombauts S., De Moor B., Rouzé P., Moreau Y., 2001.
A higher order background model improves the detection of regulatory elements by Gibbs Sampling,