Tools for matrices

Once you have found some known binding sites:
 * Plot them:
 * Delila tools: Old but not very usable. I suggest you avoid them.
 * Weblogo: The best tool on the web to generate logos
 * Enologos: Some advantages over weblogo, can plot matrices, but not in transfac format


 * Compare them:
 * T-Reg comparator: Compares against your motifs or an internal database of Transfac+Jaspar
 * CompareACE as part of AlignACE
 * MatCompare: As part of CREAD