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CUDASW++ on Tesla GPUs
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.
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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 SOLUTIONS
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.
RECOMMENDED HARDWARE CONFIGURATION
| Desktop Workstation Configuration | Data Center Configuration |
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WORKSTATION SOLUTIONS TESLA PERSONAL SUPERCOMPUTER For personal supercomputing at your desk
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DATA CENTER SOLUTIONS TESLA GPU COMPUTING CLUSTERS For computing with large-scale installations
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