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Benchmark pipeline for de novo motif discovery. Five state-of-the-art motif discovery tools and BaMMmotif2 learned motif models on in vivo and in vitro transcription factor binding datasets. The learned models were then assessed (I) by 5-fold cross-validation on the same type of data, (II) by cross-cell-line validation, and (III, IV) by cross-platform validations.
