Romulus is a computational method to accurately identify individual transcription factor binding sites from genome sequence information and cell-type--specific experimental data, such as DNase-seq. It combines the strengths of its predecessors, CENTIPEDE and Wellington, while keeping the number of free parameters in the model robustly low. The method is unique in allowing for multiple binding states for a single transcription factor, differing in their cut profile and overall number of DNase I cuts.
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