Table 11 Run time, in HH:mm:ss, for random sequences using our Java implementations on our Intel I7 platform
From: Cache and energy efficient algorithms for Nussinov’s RNA Folding
SeqLength | Classical | Transpose | ByRow | ByBox | RvsC | RvsT | BvsC | BvsT |
|---|---|---|---|---|---|---|---|---|
4000 | 0:01:01 | 0:00:29 | 0:00:34 | 0:00:09 | 44.54% | -16.54% | 85.29% | 69.10% |
8000 | 0:10:12 | 0:03:51 | 0:04:31 | 0:01:11 | 55.79% | -17.19% | 88.46% | 69.41% |
12,000 | 0:30:03 | 0:12:54 | 0:14:43 | 0:03:55 | 50.99% | -14.18% | 86.94% | 69.57% |
16,000 | 1:10:05 | 0:30:44 | 0:35:27 | 0:09:19 | 49.40% | -15.36% | 86.70% | 69.67% |
20,000 | 2:10:22 | 0:59:25 | 1:07:14 | 0:18:15 | 48.43% | -13.15% | 86.00% | 69.29% |
24,000 | 5:33:02 | out of memory | 2:19:19 | 0:42:07 | 58.17% | 87.35% | ||
28,000 | 7:22:37 | out of memory | 3:44:46 | 1:06:56 | 49.22% | 84.88% |