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UGENE on Tesla GPUs
Unipro UGENE is a free cross-platform bioinformatics software package that integrates multiple popular biological tools within a single flexible user interface. In order to provide maximum possible performance, UGENE utilizes modern NVIDIA Tesla GPUs to optimize computational routines. UGENE includes CUDA-accelerated Smith Waterman algorithm implementation and an extremely fast short DNA sequence aligner optimized for CUDA GPUs.
Download and Installation
- Download Unipro UGENE
- Works out-of-the-box on MS Windows, Linux and Mac OS X
- Includes CUDA-accelerated Smith-Waterman algorithm and fast short read aligner
- UGENE User Manual (installation and documentation)
Benchmark Data
CUDA-accelerated Smith-Waterman provides 9x speedup compared to parallel implementation of algorithm (as included into UGENE package) and 40x speedup compared to classic implementation. Details can be found on the UGENE Benchmarking page.
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Technical Papers And Presentations
- Tech-report: “Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project”
- More publications on accelerating bio-informatics applications using GPUs
Discussion Forums
Interviews / Videos
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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