Table 4.
Performance results Performance results for random RNA sequences and comparison to pknotsRE. The performance of pknotsRG-loc is similar to pknotsRG-mfe and therefore not shown. The bounded version restricts pseudoknots to a maximum length of 150 nucleotides; measured on an UltraSPARC CPU with 450 MHz and 4 GB main memory. Time is measured in (h:m:s), memory in MB.
| Length | pknotsRE | pknotsRG-mfe | pknotsRG-enf | pknotsRG-enf bounded | ||||
| Time | Mem. | Time | Mem. | Time | Mem. | Time | Mem. | |
| 40 | 17.4 | - | 0.7 | 1 | 0.9 | 2 | 0.9 | 2 |
| 80 | 21:11 | 38 | 9.5 | 5 | 8.7 | 5 | 8.8 | 5 |
| 100 | 1:23:50 | 80 | 20.0 | 8 | 32.5 | 10 | 34.5 | 9 |
| 200 | - | - | 6:46 | 36 | 8:03 | 42 | 6:33.6 | 42 |
| 300 | - | - | 33:07 | 80 | 44:58 | 102 | 20:48.4 | 90 |
| 400 | - | - | 1:48:08 | 146 | 2:28:18 | 184 | 45:28.9 | 155 |