Tregwiki:Andrew sent a comment
You may have missed a standalone program I wrote. The storm program is written in C++, and available open source as part of the cread package (cread.sf.net). It uses the same format for matrices as does TRANSFAC, and is very good if you have lots of matrices to search for in the same sequences because it pre-processes them as suffix trees. If you choose to try storm, I'll help in any way I can. Also, we have plans to turn all the useful objects in cread into C++ extensions for python, but have not had the time yet.