Table 5.
CPU usage time for PKNOTS, NUPACK, pknotsRG and HPknotter, where in our testing computer environment, PKNOTS and NUPACK cannot deal with the sequences of length >220 and 180 bp, respectively, owing to the running out of memory
| Length (bp) | PKNOTS | NUPACK | pknotsRG | HPknotter (General class) | HPknotter (Specific class) | ||||
|---|---|---|---|---|---|---|---|---|---|
| PKNOTS-kernel | NUPACK-kernel | pknotsRG-kernel | PKNOTS-kernel | NUPACK-kernel | pknotsRG-kernel | ||||
| 84 | 7.3 min | 13.1 s | 0.05 s | 31 s | 27 s | 26 s | 9 s | 7 s | 6 s |
| 105 | 35 min | 44.7 s | 0.1 s | 2.2 min | 35 s | 29 s | 38 s | 10 s | 8 s |
| 200 | 72 h | — | 0.8 s | 5.2 min | 1.8 min | 1.5 min | 1.6 min | 33 s | 30 s |
| 341 | — | — | 7.4 s | 7.1 min | 2.4 min | 2.3 min | 2.2 min | 46 s | 45 s |
| 946 | — | — | 10.1 min | 13.8 min | 7.5 min | 6.9 min | 4.1 min | 2.2 min | 2.1 min |
| 1340 | — | — | 43.5 min | 35.3 min | 11.6 min | 10.9 min | 11.6 min | 3.1 min | 2.5 min |