Figure 3.

Smith-Waterman in CUDA running on single and double GPU vs. BLAST and SSEARCH. Substitution matrix used: BLOSUM50. Gap-open penalty: 10. Gap-extension penalty: 2.

Database used: SwissProt (Dec. 2006 – 250,296 proteins and 91,694,534 amino acids).

* Smith-Waterman in CUDA running on an NVidia GeForce 8800 GTX

** Smith-Waterman in CUDA running on two NVidia GeForce 8800 GTX

Manavski and Valle BMC Bioinformatics 2008 9(Suppl 2):S10   doi:10.1186/1471-2105-9-S2-S10