Tools for matrices
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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