  We develop, analyze and experiment with a new tool, called MADMX, which
extracts frequent motifs, possibly including don't care characters, from
biological sequences. We introduce density, a simple and flexible measure for
bounding the number of don't cares in a motif, defined as the ratio of solid
(i.e., different from don't care) characters to the total length of the motif.
By extracting only maximal dense motifs, MADMX reduces the output size and
improves performance, while enhancing the quality of the discoveries. The
efficiency of our approach relies on a newly defined combining operation,
dubbed fusion, which allows for the construction of maximal dense motifs in a
bottom-up fashion, while avoiding the generation of nonmaximal ones. We provide
experimental evidence of the efficiency and the quality of the motifs returned
by MADMX
