Efficient and accurate P-value computation for Position Weight Matrices
TFM-Pvalue solves the P-value calculation problem for Position Weight Matrices and Position Specific Scoring Matrices. It can compute the P-value corresponding to a given score threshold, or conversely find the score given the desired P-value.
Matrices used have the same form as those available in the Transfac or Jaspar databases for transcription factors binding sites, for example.
Download
TFM-Pvalue is written in C++ and freely distributed under the GPL 2 license. A ReadMe file in the archive explains how to install it, how to run it and how to understand the output.
R package
TFM-pvalue is also available as an R package on the CRAN.
Python package
TFM-pvalue is also available as a Python package here (by Jared Andrews).
Reference
Efficient and accurate P-value computation for Position Weight Matrices
H. Touzet and J.S. Varré
Algorithms for Molecular Biology 2007, 2:15