MAD is a python package that provides tools for locating and analyzing candidate regulatory motifs (factor binding sites) using PWMs. MAD provides tools for the visualization of motifs in genomic sequences (intergenic or otherwise) with their appropriate significance. It also provides algorithms for optimizing (refining) motif PWMs based on clustering results (coexpression), phylogenetic information (orthology across genomes), and cooperativity with other motifs.
Visualization