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De novo motif discovery is a difficult computational task. Historically, dedicated algorithms always reported a high percentage of false positives. Their performance did not improve considerably even after they adapted to handle large amounts of chromatin immunoprecipitation sequencing (ChIP-Seq) data.
(Lihu and Holban, 2015) A review of ensemble methods for de novo motif discovery in ChIP-Seq data. Brief Bioinform.