From: Cache and energy efficient algorithms for Nussinov’s RNA Folding
SeqLength | Classical | Transpose | ByRow | ByBox | RvsC | RvsT | BvsC | BvsT |
---|---|---|---|---|---|---|---|---|
4000 | 0:01:29 | 0:00:49 | 0:00:49 | 0:00:13 | 45.18% | 1.62% | 85.72% | 74.37% |
8000 | 0:14:38 | 0:06:34 | 0:06:29 | 0:01:38 | 55.70% | 1.30% | 88.86% | 75.17% |
12,000 | 0:46:36 | 0:21:44 | 0:21:37 | 0:05:36 | 53.60% | 0.55% | 87.98% | 74.23% |
16,000 | 1:56:26 | 0:51:22 | 0:51:22 | 0:13:16 | 55.88% | -0.02% | 88.60% | 74.16% |
20,000 | 3:39:36 | 1:40:09 | 1:40:05 | 0:26:10 | 54.42% | 0.06% | 88.08% | 73.87% |
24,000 | 6:29:22 | 2:52:43 | 2:52:54 | 0:44:43 | 55.59% | -0.11% | 88.52% | 74.11% |
28,000 | 8:05:15 | 4:33:21 | 4:35:04 | 1:10:48 | 43.32% | -0.62% | 85.41% | 74.10% |