Tag: GPU

G-PAS 2.0 – Fast GPU vesion of a Pairwise Alignment algorithms

G-PAS 2.0

:: DESCRIPTION

G-PAS (gpu-pairAlign) implements global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. Our solution performs the alignment of every given sequence pair, which is a required step e.g. for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Tests show that the implementation, with performance up to 6.3 GCUPS on a single GPU for affine gap penalties, is very efficient in comparison to other CPU and GPU-based solutions.

::DEVELOPER

G-PAS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • g++ compiler
  • CUDA 2.0 or higher
  • CUDA-compliant GPU

:: DOWNLOAD

 G-PAS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 20;12:181.
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.
Blazewicz J, Frohmberg W, Kierzynka M, Pesch E, Wojciechowski P.

motifGPU 1.0 – GPU-computing Accelerate Motif Analysis

motifGPU 1.0

:: DESCRIPTION

motifGPU is a library that uses GPUs to accelerate motif search. Extensive performance comparison studies on two different graphics cards from NVIDIA, (GeForce) GTX 260 and GeForce GTX 480, showed that commonly-used model-based motif scan procedures can be dramatically accelerated using our library. De novo motif discovery can also benefit from our GPU-accelerated tools.

::DEVELOPER

Steve Qin @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  motifGPU

:: MORE INFORMATION

For bug report, questions or comments, please contact Pooya Zandevakili (zandv@umich.edu).