Finding DNA motifs with universalmotif

A very common task when working with DNA sequences is finding instances of motifs – a short-defined sequence – within a longer sequence. These could represent protein-DNA binding sites such as transcription factor binding sites in a gene promoter or enhancer region. There are two starting points for this analysis – you either have a database of motifs that you want 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.

Getting ready

For this recipe, we need a matrix describing the motif (a position-specific weight matrix or PWSM) and a set of sequences from upstream of transcriptional start sites. These are provided in the rbioinfcookbok package. We’ll use the universalmotif package to work with motifs and...