Table 10 Run time, in HH:mm:ss, for random sequences using our Java implementations on our AMD platform
From: Cache and energy efficient algorithms for Nussinov’s RNA Folding
SeqLength | Classical | Transpose | ByRow | ByBox | RvsC | RvsT | BvsC | BvsT |
|---|---|---|---|---|---|---|---|---|
4000 | 0:06:10 | 0:00:54 | 0:01:03 | 0:00:21 | 82.90% | -18.00% | 94.23% | 60.20% |
8000 | 2:01:55 | 0:06:27 | 0:07:43 | 0:02:46 | 93.68% | -19.42% | 97.73% | 57.22% |
12,000 | 8:48:01 | 0:26:02 | 0:29:56 | 0:09:12 | 94.33% | -14.97% | 98.26% | 64.64% |
16,000 | 18:45:51 | out of memory | 1:07:26 | 0:26:48 | 94.01% | 97.62% | ||
20,000 | 35:02:59 | out of memory | 2:04:00 | 0:48:39 | 94.10% | 97.69% |