Table 2

Smith-Waterman in CUDA running on single and double GPU vs. BLAST and SSEARCH

Sequence

SW-Cuda*

SW-Cuda**

Ssearch(Fasta)

Blast

Name

Length

Time (s)

MCUPS

Time (s)

MCUPS

Time (s)

MCUPS

Time (s)

MCUPS


O29181

63

2.98

1849

1.547

3561

46

119

3.7

1488

P03630

127

5.88

1889

3.075

3612

93

119

5.7

1948

P53765

255

12.31

1811

6.505

3428

184

121

11

2027

Q8ZGB4

361

17.44

1810

9.162

3446

275

114

16.3

1936

P58229

511

24.89

1795

13.326

3353

362

123

16.6

2691


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