Tregwiki:Andrew sent a comment

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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 ( 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.

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