|
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 |
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