Table 3 Prediction results of the IP-based method (σ = 0.7) and prediction results of the other algorithms.
From: Prediction of RNA secondary structure with pseudoknots using integer programming
PKB num. | Length | Sensitivity (%) | Specificity (%) | ||||||
|---|---|---|---|---|---|---|---|---|---|
IP | ILM | pknotsRG | PKNOTS | IP | ILM | pknotsRG | PKNOTS | ||
PKB115 | 21 | 100.00 | 66.67 | 100.00 | 66.67 | 100.00 | 100.00 | 100.00 | 100.00 |
PKB102 | 24 | 100.00 | 87.50 | 100.00 | 87.50 | 80.00 | 77.78 | 88.89 | 77.78 |
PKB119 | 24 | 88.89 | 0.00 | 77.78 | 66.67 | 88.89 | 0.00 | 87.50 | 100.00 |
PKB103 | 25 | 100.00 | 57.14 | 57.14 | 42.86 | 70.00 | 66.67 | 50.00 | 50.00 |
PKB123 | 26 | 90.00 | 90.00 | 70.00 | 60.00 | 90.00 | 90.00 | 77.78 | 85.71 |
PKB154 | 26 | 100.00 | 90.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
PKB152 | 26 | 100.00 | 90.00 | 100.00 | 100.00 | 90.91 | 90.00 | 90.91 | 90.91 |
PKB126 | 27 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 | 100.00 |
PKB124 | 29 | 100.00 | 70.00 | 100.00 | 70.00 | 100.00 | 100.00 | 100.00 | 100.00 |
PKB100 | 31 | 100.00 | 91.67 | 91.67 | 100.00 | 92.31 | 91.67 | 91.67 | 100.00 |
PKB105 | 32 | 88.89 | 88.89 | 88.89 | 88.89 | 88.89 | 100.00 | 100.00 | 100.00 |
PKB118 | 33 | 90.00 | 80.00 | 90.00 | 80.00 | 81.82 | 72.73 | 81.82 | 72.73 |
PKB120 | 36 | 100.00 | 100.00 | 100.00 | 100.00 | 85.71 | 100.00 | 100.00 | 100.00 |
PKB65 | 46 | 93.33 | 93.33 | 0.00 | 73.33 | 70.00 | 87.50 | 0.00 | 68.75 |
PKB205 | 48 | 23.08 | 0.00 | 23.08 | 23.08 | 15.00 | 0.00 | 23.08 | 23.08 |
PKB147 | 51 | 77.78 | 55.56 | 50.00 | 50.00 | 63.64 | 55.56 | 47.37 | 52.94 |
PKB248 | 66 | 80.00 | 65.00 | 35.00 | 65.00 | 64.00 | 72.22 | 33.33 | 61.90 |
PKB72 | 67 | 100.00 | 0.00 | 35.29 | 100.00 | 62.96 | 0.00 | 31.58 | 73.91 |
PKB140 | 69 | 73.91 | 65.22 | 13.04 | 43.48 | 62.96 | 65.22 | 15.79 | 50.00 |
PKB143 | 71 | 62.50 | 91.67 | 29.17 | 70.83 | 48.39 | 78.57 | 29.17 | 68.00 |
PKB144 | 71 | 79.17 | 95.83 | 29.17 | 66.67 | 70.37 | 95.83 | 31.82 | 72.73 |
PKB173 | 73 | 63.64 | 77.27 | 36.36 | 77.27 | 50.00 | 68.00 | 44.44 | 77.27 |
PKB276 | 73 | 42.86 | 76.19 | 33.33 | 38.10 | 30.00 | 80.00 | 30.43 | 38.10 |
PKB275 | 85 | 65.38 | 96.15 | 15.38 | 50.00 | 50.00 | 83.33 | 15.38 | 72.22 |
PKB75 | 88 | 71.88 | 93.75 | 18.75 | 81.25 | 62.16 | 85.71 | 22.22 | 81.25 |
PKB76 | 89 | 56.00 | 100.00 | 52.00 | 44.00 | 40.00 | 69.44 | 48.15 | 34.38 |
PKB164 | 96 | 38.71 | 74.19 | 48.39 | 35.48 | 29.27 | 65.71 | 53.57 | 34.38 |
PKB168 | 105 | 61.76 | 79.41 | 35.29 | 76.47 | 50.00 | 81.82 | 34.29 | 86.67 |
PKB252 | 110 | 15.38 | 97.44 | 35.90 | 97.44 | 13.04 | 80.85 | 35.90 | 92.68 |
PKB191 | 113 | 74.36 | 82.05 | 56.41 | 71.79 | 61.70 | 80.00 | 55.00 | 73.68 |
PKB135 | 116 | 82.05 | 84.62 | 38.46 | 74.36 | 69.57 | 84.62 | 40.54 | 74.36 |
PKB236 | 120 | 50.00 | 37.50 | 0.00 | 67.50 | 42.55 | 30.61 | 0.00 | 72.97 |
PKB137 | 133 | 70.45 | 84.09 | 63.64 | 86.36 | 65.96 | 80.43 | 63.64 | 86.36 |
PKB134 | 137 | 40.91 | 59.09 | 40.91 | 84.09 | 33.33 | 50.00 | 41.86 | 80.43 |
Average | 75.91 | 74.12 | 54.85 | 71.74 | 65.40 | 73.07 | 54.89 | 75.09 | |