Table 1 Run time (HH:mm:ss) for random sequences on Xeon E5 platform
From: Cache and energy efficient algorithms for Nussinov’s RNA Folding
SeqLength | Classical | Transpose | ByRow | ByBox | RvsC | RvsT | BvsC | BvsT |
|---|---|---|---|---|---|---|---|---|
4000 | 0:02:02 | 0:00:20 | 0:00:13 | 0:00:11 | 89.13% | 35.18% | 90.79% | 45.03% |
8000 | 0:14:49 | 0:02:35 | 0:01:44 | 0:01:18 | 88.30% | 33.10% | 91.26% | 50.00% |
12,000 | 0:37:51 | 0:08:33 | 0:05:51 | 0:04:05 | 84.55% | 31.61% | 89.20% | 52.17% |
16,000 | 1:12:49 | 0:20:08 | 0:13:47 | 0:09:22 | 81.08% | 31.55% | 87.14% | 53.49% |
20,000 | 2:33:39 | 0:38:54 | 0:26:48 | 0:17:49 | 82.56% | 31.12% | 88.41% | 54.22% |
24,000 | 3:38:09 | 1:07:00 | 0:45:15 | 0:30:10 | 79.26% | 32.46% | 86.17% | 54.98% |
28,000 | 5:57:03 | 1:46:00 | 1:12:01 | 0:47:18 | 79.83% | 32.06% | 86.75% | 55.37% |
32,000 | - | 2:37:50 | 1:47:28 | 1:09:58 | - | 31.91% | - | 55.68% |
36,000 | - | 3:44:51 | 2:35:58 | 1:38:50 | - | 30.63% | - | 56.05% |
40,000 | - | 5:08:10 | 3:33:43 | 2:14:38 | - | 30.65% | - | 56.31% |