TFM-CUDA

CUDA tools for Position Weight Matrices (PWMs)

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

The method is described in the paper referenced below, and uses parallelism on graphics processing units (GPUs). TFM-CUDA was designed to speed-up some commonly computations on PWMs. If you prefer full-featured tools, please use TFM-Scan and TFM-Pvalue.

Download

TFM-CUDA needs the NVIDIA CUDA SDK. A ReadMe file is provided in the archive.

• TFM-CUDA-0.4.tar.gz (2009/11/30)
• TFM-CUDA-0.3.tar.gz (2009/04/10)
• TFM-CUDA-0.2.tar.gz (2009/01/27)
• TFM-CUDA-0.1.tar.gz (2008/12/01)

See the Changelog.

References

• Parallel Position Weight Matrices Algorithms
  M. Giraud and J.S. Varré
  International Symposium on Parallel and Distributed Computing (ISPDC 2009), 65-69, 10.1109/ISPDC.2009.31, 2009 [abstract]
• An extended article is in submission to Parallel Computing.