Table 3

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

Sequence

SW-Cuda*

SW-Cuda**

Farrar

Name

Length

Time (s)

MCUPS

Time (s)

MCUPS

Time (s)

MCUPS


P02232

143

5.59

1845

2.95

3497

9

1149

P01111

189

7.59

1796

3.84

3551

10

1367

P05013

189

7.59

1796

3.84

3551

10

1367

P14942

222

8.84

1812

4.48

3575

12

1338

P00762

246

9.85

1802

5.01

3542

13

1369

P10318

362

14.71

1775

7.57

3450

15

1746

P07327

374

15.28

1766

7.86

3433

16

1691

P01008

464

18.96

1765

9.83

3405

18

1864

P10635

497

20.39

1758

10.43

3438

19

1892

P25705

553

22.83

1747

11.88

3358

19

2105

P03435

567

23.32

1754

11.96

3420

20

2045


Substitution matrix used: BLOSUM50. Gap-open penalty: 10. Gap-extension penalty: 2.

Database used: SwissProt (Rel. 49.1 – 208,005 proteins and 75,841,138 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