Table 1

Smith-Waterman in CUDA running on single and double GPU vs. Liu's solution implemented in OpenGL

Sequence

SW-Cuda*

SW-Cuda**

Weiguo Liu

Name

Length

MCUPS

MCUPS

MCUPS


O29181

63

1849

3561

197

P03630

127

1889

3612

317

P53765

255

1811

3428

428

Q8ZGB4

361

1810

3446

486

P58229

511

1795

3353

533


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

Open Data