Tag: Smith Waterman

SWAPHI 1.0.5 – Smith-Waterman on Intel Xeon Phi

SWAPHI 1.0.5

:: DESCRIPTION

SWAPHI is the first parallel algorithm to accelerate the Smith-Waterman protein database search on Intel Xeon Phi coprocessors (with affine gap penalty).

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SWAPHI

:: MORE INFORMATION

Citation:

Yongchao Liu and Bertil Schmidt:
“SWAPHI: Smith-Waterman protein database search on Xeon Phi coprocessors”.
25th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2014), 2014, accepted

CUDASW++ 3.1.2 – Parallel Smith Waterman Protein database search algorithm

CUDASW++ 3.1.2

:: DESCRIPTION

CUDASW++ (compute unified device architecture) is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA toolkits and SDK 2.0 or higher.

:: DOWNLOAD

 CUDASW++

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
“CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions“.
BMC Research Notes, 2010, 3:93

SWCuda 1.92 – CUDA compatible for Smith-Waterman Sequence Alignment

SWCuda 1.92

:: DESCRIPTION

SWCuda (SmithWaterman-CUDA)allows to perform alignments between one or more sequences and a database (all the sequences, even in the DB, are intended to be proteinic). It is implemented in the recently released CUDA programming environment by NVidia.

::DEVELOPER

Svetlin A. Manavski, Giorgio Valle,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • NVIDIA CUDA SDK

:: DOWNLOAD

  SWCuda

:: MORE INFORMATION

Citation

Svetlin A. Manavski, Giorgio Valle,
“CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment“,
BMC Bioinformatics 2008, 9(Suppl 2):S10 (26 March 2008)