|
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 |
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