Figure 2.

Motif discovery pipeline. Pipeline for motif discovery based on genome-wide evidence of regulation. Sequence reads are aligned to the reference genome and peak calling is executed to produce a set of putative regulatory regions (for example, DNaseI peaks) and corresponding evidence of regulation (for example, ChIP-seq peaks). As a final step in the pipeline, cERMIT is run on the preprocessed data to produce motif predictions that are best supported by the observed experimental evidence E.