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 two distinct structured motif discovery algorithms: MUSA and RISO.

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).

RISO, another complex motif extraction tool, searches for complex motifs with certain characteristics specified by the user, through the assignment of a set of parameters such as the number and sizes of the boxes that form the structured motif, the distances between them and the minimum quorum expected. It is also possible to specify a number of substitutions for each box. Like MUSA, RISO also requires the list of genes whose promoters are to be searched for motifs, and returns the list of motifs found and their corresponding quorums.