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In this protocol we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motifdoi:10.1007/978-1-4939-6396-6_19 pmid:27557775 fatcat:uf4jvjkdw5ed5h4jy6bhwui3si