DISCOVERER provides tools for the purpose of motif extraction: the identification of de novo binding site consensus sequences from a given set of non-coding DNA sequences (such as the promoter regions of a gene). DISCOVERER contains a structured motif discovery algorithms: MUSA.

Contrary to many modern motif finders, MUSA (Motif finding using an UnSupervised Approach) does not require the user to specify parameters (such as box lengths and distances between boxes) in order to extract motifs. The algorithm can therefore either be used autonomously to search for motifs, or to estimate the search parameters to be used in other motif discovery tools. Requiring as input a list of genes, MUSA returns the list of structured or simple motifs found, ordered by their p-value, and the proportion of sequences containing each motif (the quorum).