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