Fast matching of Position Weight Matrices
TFM-scan is an efficient program for finding instances of patterns given as position specific scoring matrices or position weight matrices in DNA sequences. It can handle large sets of matrices, such as those available in the Transfac or Jaspar databases and allows for genome-scale analysis. TFM-Scan is also able to cluster similar matrices and similar occurrences.
TFM-Scan2014.5.9.tar.gz, updated on 5-9-2014
TFM-scan is implemented in C++ and freely distributed under the GPL 2 license. The archive contains a readme file with detailed instructions.
Large scale matching for Position Weight Matrices
Liefooghe A., Touzet H. and Varré J.-S.
CPM (Combinatorial Pattern Matching), volume 4009 of Lecture Notes in Computer Science, p. 401-412, 2006.