Table 2.
Results of MCTS-RNA, antaRNA and MODENA for individual Rfam targets
| Data | MCTS-RNA | antaRNA | MODENA | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Rfam | RfamID | N | ℓ | Sc | E t | Sc | E t | Sc | E t |
| RF00001 | 5S_rRNA | 117 | 83 | 44/50 | 196.87 | 4/50 | 28.87 | 0/50 | – |
| RF00002 | 5_8S_rRNA| | 151 | 127 | 41/50 | 166.06 | 0/50 | – | 13/50 | 64.62 |
| RF00003 | U1 | 161 | 121 | 5/50 | 371.86 | 0/50 | – | 50/50 | 84.43 |
| RF00004 | U2 | 193 | 149 | 50/50 | 3.4 | 50/50 | 20.04 | 50/50 | 130.99 |
| RF00005 | tRNA | 74 | 53 | 50/50 | 0.15 | 50/50 | 0.64 | 50/50 | 32.25 |
| RF00006 | Vault | 89 | 69 | 50/50 | 0.38 | 50/50 | 3.65 | 50/50 | 37.49 |
| RF00007 | U12 | 154 | 112 | 50/50 | 10.08 | 19/50 | 8.19 | 49/50 | 76.19 |
| RF00008 | Hammerhead_3 | 54 | 39 | 50/50 | 0.49 | 50/50 | 0.33 | 50/50 | 28.32 |
| RF00009 | RNaseP_nuc | 348 | 293 | 48/50 | 84.58 | 0/50 | – | 0/50 | – |
| RF00010 | RNaseP_bact_a | 357 | 255 | 0/50 | – | 0/50 | – | 0/50 | – |
| RF00011 | RNaseP_bact_b | 382 | 286 | 0/50 | – | 0/50 | – | 0/50 | – |
| RF00012 | U3 | 215 | 176 | 50/50 | 5.64 | 50/50 | 30.6 | 50/50 | 197.66 |
| RF00013 | 6S | 185 | 137 | 50/50 | 31.05 | 46/50 | 12.83 | 50/50 | 124.12 |
| RF00014 | DsrA | 87 | 58 | 50/50 | 0.1 | 44/50 | 0.78 | 42/50 | 40.6 |
| RF00015 | U4 | 140 | 109 | 50/50 | 2.07 | 22/50 | 10.59 | 49/50 | 62.18 |
| RF00016 | SNORD14 | 129 | 112 | 0/50 | – | 0/50 | – | 0/50 | – |
| RF00017 | SRP_euk_arch4 | 301 | 200 | 49/50 | 133.19 | 44/50 | 56.24 | 50/50 | 452.17 |
| RF00018 | CsrB | 360 | 311 | 0/50 | – | 0/50 | – | 0/50 | – |
| RF00019 | Y_RNA | 83 | 60 | 50/50 | 1.51 | 49/50 | 1.67 | 50/50 | 36.32 |
| RF00020 | U5 | 119 | 89 | 0/50 | – | 0/50 | – | 0/50 | – |
| RF00021 | Spot_42 | 118 | 81 | 50/50 | 0.26 | 50/50 | 0.98 | 50/50 | 55.34 |
| RF00022 | GcvB | 148 | 115 | 50/50 | 1.34 | 49/50 | 10.04 | 50/50 | 74.6 |
| RF00024 | Telomerase-vert | 451 | 346 | 0/50 | – | 0/50 | – | 0/50 | – |
| RF00025 | Telomerase-cil | 210 | 173 | 50/50 | 4.88 | 22/50 | 71.32 | 50/50 | 170.58 |
| RF00026 | U6 | 102 | 97 | 50/50 | 1.6 | 50/50 | 3.37 | 50/50 | 84.66 |
| RF00027 | let-7 | 79 | 48 | 50/50 | 0.19 | 50/50 | 0.76 | 50/50 | 37.35 |
| RF00028 | Intron_gp | 344 | 291 | 7/50 | 336.39 | 0/50 | – | 0/50 | – |
| RF00029 | Intron_gpI | 73 | 54 | 50/50 | 2.16 | 14/50 | 7.49 | 50/50 | 35.46 |
| RF00030 | RNase_MRP | 340 | 276 | 50/50 | 19.96 | 31/50 | 298.74 | 50/50 | 414.19 |
| Total | 1045/1450 | 744/1450 | 953/1450 | ||||||
The GC content is controlled to 0.5 and the time limit is set to 10 min. N denotes the length of the target structure. ℓ describes the sum of the number of base pairs and that of free bases in the target structure. For each method, the number of successes in 50 runs is shown as Sc, and E t indicates the average time (in seconds) required to find a compliant sequence. If no compliant sequences are found, it is left blank