Instance | Length | BAR |
BFS
|
TABU
|
EA
|
HIPATH
|
HIPATH2
|
---|
| | | (k = 10) | (n = 1000) | | | |
---|
rb1 | 148 nt | - | 24.04 | 24.04 | 23.2 |
20.94
|
20.94
|
rb2 | 113 nt | * | 8.2 | 7.25 |
6.5
| 6.6 | 6.6 |
rb3 | 141 nt | - | 22.4 | 17.9 | 17.5 |
16.7
|
16.7
|
rb4 | 146 nt | - |
16.9
|
16.9
|
16.9
|
16.9
|
16.9
|
rb5 | 201 nt | - | 24.54 | 24.54 |
21.44
|
21.44
|
21.44
|
hok | 396 nt | - | 28.5 | 29.66 |
20.7
| 21.1 | 21.1 |
SL | 56 nt |
11.8
| 13 | 12.9 | 13 | 12.4 | 12.4 |
attenuator | 73 nt |
8.3
| 8.7 | 8.6 | 8.7 | 8.6 | 8.5 |
s15 | 74 nt |
6.6
| 7.1 |
6.6
| 7.1 | 7.1 |
6.6
|
sbox leader | 247 nt | * |
5.2
|
5.2
|
5.2
|
5.2
|
5.2
|
thiM leader | 165 nt | - | 16.13 | 14.84 |
12.3
| 14 | 12.4 |
ms2 | 73 nt | * |
6.6
|
6.6
|
6.6
|
6.6
|
6.6
|
HDV | 153 nt | - | 17.4 | 17 | 16.8 |
15.6
|
15.6
|
dsrA | 85 nt |
8
| 8.3 | 8.2 |
8
| 8.3 |
8
|
ribD leader | 304 nt | - | 10.71 |
9.5
|
9.5
| 10.71 |
9.5
|
amv | 145 nt | * | 5.8 | 5.8 | 5.74 | 5.8 |
5.5
|
alpha operon | 130 nt | * | 6.5 | 6.5 | 6.1 | 6.5 |
5.96
|
HIV-1 leader | 280 nt | - | 9.3 | 11.3 |
8.9
| 9.3 | 9.3 |
- The dataset was taken from [12, 19], the results for BFS and RNATABUPATH from [12] and the results for EA from [13]. Energy barriers are given in kcal/mol. The maxkeep value k was 10 for BFS itself and for the BFS used within HIPATH and HIPATH2. HIPATH2 was used with auto-adjusted fuzzy related hishape numbers, π
a
and θ=1.5. HIPATH was used with the default parameters. Bold numbers represent the minimum value for the respective sequence. The symbol "*" means BARRIERS could not be applied because either the start or the target structure was not locally optimal. The symbol "-" means computation did not finish within one day. The energy range used with RNASUBOPT for BARRIERS was determined using HIPATH2 and set to the barrier energy of HIPATH2 + 1 kcal/mol. Note that the results may be different from the ones shown in [14] since the used start and target structures may differ. Here we used the ones provided in [12], while in [14] we derived them for ourselves.