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De-novo motif search is a frequently applied bioinformatics procedure to identify and prioritize recurrent elements in sequences sets for biological investigation, such as the ones derived from high-throughput differential expression experiments. Several algorithms have been developed to perform motif search, employing widely different approaches and often giving divergent results.
(Dassi and Quattrone 2016) DynaMIT: the dynamic motif integration toolkit. Nucleic Acids Res.