Tag: Position Weight Matrices

TFM-CUDA 0.5 – CUDA tools for Position Weight Matrices (PWMs)

TFM-CUDA 0.5

:: DESCRIPTION

TFM-CUDA is a CUDA implementation of parallel algorithms able to:

  • scan a matrix or a set of matrices against a sequence (see also TFM-Scan),
  • compute the P-value corresponding to a score, or the score corresponding to a Pvalue (see also TFM-Pvalue),
  • compare two matrices

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

 TFM-CUDA

:: MORE INFORMATION

Citation

Mathieu Giraud and Jean-Stéphane Varré,
Parallel Position Weight Matrices Algorithms,
Parallel Computing, 10.1016/j.parco.2010.10.001

TFM-Pvalue 0.0.8 – Efficient and Accurate P-value Computation for Position Weight Matrices

TFM-Pvalue 0.0.8

:: DESCRIPTION

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.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R

 TFM-Pvalue

:: MORE INFORMATION

Citation

Efficient and accurate P-value computation for Position Weight Matrices
H. Touzet and J.S. Varré
Algorithms for Molecular Biology 2007, 2:15