Finding regulatory sequences in DNA: motif discovery

The purpose of motif discovery as discussed here is to find binding sites of DNA binding regulators. We assume that the binding sites are short segments of DNA, not necessarily contiguous, to which a specific (family of) transcription factors can bind. While such sites may appear in genic as well as inter­genic regions, we focus here on finding binding sites only in the promoter region of each gene. It’s worthwhile to note that the existence of a binding site is no guarantee that the site (the corresponding TF) plays a role in regulating the gene in question; the site may not be accessible due to chromatin structure, may never be occupied due to resource constraints and higher affinity sites elsewhere, and so on. Nevertheless, knowing who could participate in regulating each gene, and finding where they bind at a base­pair resolution, is a useful source of information.