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.
- C++ compiler
- NVIDIA CUDA SDK
:: MORE INFORMATION
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)