Table 2 Run time (HH:mm:ss) for real RNA sequences of [20] on Xeon E5 platform
From: Cache and energy efficient algorithms for Nussinov’s RNA Folding
Code | SeqLength | Classical | Transpose | ByRow | ByBox | RvsC | RvsT | BvsC | BvsT |
|---|---|---|---|---|---|---|---|---|---|
NM_178697.5 | 4008 | 0:02:17 | 0:00:20 | 0:00:13 | 0:00:11 | 90.38% | 35.19% | 91.93% | 45.66% |
XM_018415261.1 | 8011 | 0:11:56 | 0:02:36 | 0:01:44 | 0:01:17 | 85.45% | 33.28% | 89.30% | 50.95% |
XM_018223360.1 | 11,995 | 0:34:06 | 0:08:34 | 0:05:49 | 0:04:02 | 82.96% | 32.16% | 88.17% | 52.92% |
NM_003458.3 | 15,964 | 1:17:17 | 0:19:59 | 0:13:38 | 0:09:09 | 82.36% | 31.77% | 88.15% | 54.18% |
XM_018221838.1 | 19,957 | 2:32:50 | 0:38:39 | 0:26:36 | 0:17:25 | 82.60% | 31.19% | 88.61% | 54.95% |
XM_007787868.1 | 24,003 | 4:24:21 | 1:06:57 | 0:46:14 | 0:29:53 | 82.51% | 30.94% | 88.70% | 55.37% |
LH929943.1 | 28,029 | 7:04:35 | 1:46:18 | 1:13:34 | 0:46:59 | 82.67% | 30.80% | 88.93% | 55.80% |
XM_007916465.1 | 32,040 | - | 2:38:22 | 1:49:50 | 1:09:47 | - | 30.65% | - | 55.93% |
JL711896.1 | 35,962 | - | 3:44:10 | 2:35:14 | 1:37:39 | - | 30.75% | - | 56.44% |
AJ245616.1 | 40,003 | - | 5:08:02 | 3:34:06 | 2:13:44 | - | 30.49% | - | 56.58% |