Cribi-Genomics

SmithWaterman-CUDA. The GPGPU project to run Smith-Waterman algorithm on the modern GPU (s) made by NVIDIA

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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)

The source code is available here. The last version is swcuda-1.92.tgz. To make it run follow the instructions in the documentation page.


A pre-compiled binary package for Linux Fedora Core 8  is available
as well:  http://www.manavski.com/downloads/smithwaterman-cuda-fc8-1.84.tgz
For people having other Linux distributions please note the binary is compiled in the following environment:

package
version
gcc
4.1.2
glibc
2.7.2
QT
4
CUDA
1.1