Efficient and accurate P-value computation for Position Weight Matrices
TFM-Pvalue is a software suite providing tools for computing the score threshold associated to a given P-value and the P-value associated to a given score threshold. It uses Position Weight Matrices, such as those available in the Transfac or Jaspar databases.
The program takes as input a matrix, the background probabilities for the letters of the DNA alphabet and a score or a P-value. The method is described into the paper referenced below.
Availability
You could download and install a version of TFM-Pvalue on your computer (TFM-Pvalue.tar.gz). You need a C++ compiler to build it. A ReadMe file in the archive explains how to install it, how to run it and how to understand the output.
Publication
Efficient and accurate P-value computation for Position Weight Matrices
H. Touzet and J.S. Varré
Algorithms for Molecular Biology 2007, 2:15 [abstract]