CUDASW++ is a bio-informatics 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. CUDASW++ supports query lengths up to 59K.

Download and Installation

• Download CUDASW++
• CUDASW++ Release Notes (Installation, User Guide)

Benchmark Data

CUDASW++ can take advantage of multiple Tesla GPUs and runs between 10x-50x faster than NCBI BLAST, getting up to 30 GCUPs on query lengths of over 5000. Whereas BLAST is a heuristic algorithm, CUDASW++ does optimal local alignment using the Smith-Waterman algorithm.

Technical Papers

• "CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units, Y. Liu, D. Maskell, B. Schmidt: BMC Research Notes 2009, 2:73
• More publications on accelerating bio-informatics applications using GPUs

Discussion Forums

• GPU computing communities on GPUcomputing.net

The Tesla Bio Workbench applications can be deployed on GPU-based desktop personal supercomputers or in data center solutions. Built on the revolutionary massively parallel CUDA architecture, these solutions are designed to accelerate the pace of computational science.

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