MoAn is a discriminative pattern finder capable of using a very large negative set to greatly improve its predictive power. It is capable of handling sequences that are not repeat masked given that the negative set is a representative sample of promoters from the organism examined.
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Valen, E., Winther, O., Sandelin, A. and Krogh, A.
Discovery of regulatory elements is dramatically improved by a discriminatory approach.
PLoS Computational Biology 5(11) 2009