A very common task when working with DNA sequences is finding instances of motifs—a short defined sequence—in a longer sequence. These could represent protein—DNA binding sites, such as transcription factor binding sites in a gene promoter or an enhanced region. There are two start points for this analysis: either you have a database of motifs that you wish to use to scan target DNA sequences and extract wherever the motif occurs or you have just the sequences of interest and you want to find out whether there are any repeating motifs in there. We'll look at ways of doing both of these things in this recipe. We'll use the universalmotif package in both cases.