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Table of contents:
- Overview
- Performance Plots
- Performance of RNAalifold(20) - scored higher in this pairwise comparison
- Performance of HotKnots - scored lower in this pairwise comparison
- Compile and download dataset for RNAalifold(20) & HotKnots [.zip] - may take several seconds...
Overview
| Metric | RNAalifold(20) | HotKnots | |
|---|---|---|---|
| MCC | 0.644 | > | 0.577 |
| Average MCC ± 95% Confidence Intervals | 0.635 ± 0.067 | > | 0.611 ± 0.095 |
| Sensitivity | 0.491 | < | 0.514 |
| Positive Predictive Value | 0.849 | > | 0.652 |
| Total TP | 523 | < | 548 |
| Total TN | 209490 | > | 209266 |
| Total FP | 131 | < | 355 |
| Total FP CONTRA | 21 | < | 52 |
| Total FP INCONS | 72 | < | 240 |
| Total FP COMP | 38 | < | 63 |
| Total FN | 543 | > | 518 |
| P-value | 3.56938820447e-08 | ||
Performance plots
Performance of RNAalifold(20) - scored higher in this pairwise comparison
1. Total counts & total scores for RNAalifold(20)
| Total Base Pair Counts | |
|---|---|
| Total TP | 523 |
| Total TN | 209490 |
| Total FP | 131 |
| Total FP CONTRA | 21 |
| Total FP INCONS | 72 |
| Total FP COMP | 38 |
| Total FN | 543 |
| Total Scores | |
|---|---|
| MCC | 0.644 |
| Average MCC ± 95% Confidence Intervals | 0.635 ± 0.067 |
| Sensitivity | 0.491 |
| Positive Predictive Value | 0.849 |
| Nr of predictions | 28 |
2. Individual counts for RNAalifold(20) [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| 2KDQ_B | 0.60 | 0.36 | 1.00 | 4 | 402 | 0 | 0 | 0 | 0 | 7 | |
| 2L94_A | 0.53 | 0.50 | 0.59 | 10 | 973 | 7 | 0 | 7 | 0 | 10 | |
| 2WRQ_Y | 0.57 | 0.59 | 0.56 | 10 | 2832 | 11 | 5 | 3 | 3 | 7 | |
| 2XKV_B | 0.45 | 0.20 | 1.00 | 4 | 4556 | 3 | 0 | 0 | 3 | 16 | |
| 2XQD_Y | 0.88 | 0.78 | 1.00 | 21 | 2829 | 0 | 0 | 0 | 0 | 6 | |
| 2XXA_G | 0.41 | 0.17 | 1.00 | 7 | 5144 | 0 | 0 | 0 | 0 | 35 | |
| 3A2K_C | 0.86 | 0.75 | 1.00 | 21 | 2905 | 0 | 0 | 0 | 0 | 7 | |
| 3AMU_B | 0.86 | 0.74 | 1.00 | 20 | 2983 | 1 | 0 | 0 | 1 | 7 | |
| 3G4S_9 | 0.69 | 0.49 | 0.97 | 28 | 7352 | 3 | 1 | 0 | 2 | 29 | |
| 3GX2_A | 0.77 | 0.60 | 1.00 | 24 | 4347 | 1 | 0 | 0 | 1 | 16 | |
| 3IVN_B | 0.74 | 0.58 | 0.95 | 18 | 2327 | 1 | 1 | 0 | 0 | 13 | |
| 3IZ4_A | 0.53 | 0.35 | 0.82 | 46 | 70820 | 15 | 4 | 6 | 5 | 86 | |
| 3IZF_C | 0.71 | 0.59 | 0.86 | 32 | 6866 | 5 | 1 | 4 | 0 | 22 | |
| 3JYV_7 | 0.81 | 0.66 | 1.00 | 21 | 2829 | 0 | 0 | 0 | 0 | 11 | |
| 3JYX_3 | 0.60 | 0.52 | 0.70 | 14 | 6308 | 17 | 0 | 6 | 11 | 13 | |
| 3JYX_4 | 0.39 | 0.30 | 0.50 | 10 | 12226 | 15 | 0 | 10 | 5 | 23 | |
| 3LA5_A | 0.75 | 0.56 | 1.00 | 19 | 2466 | 0 | 0 | 0 | 0 | 15 | |
| 3NPB_A | 0.68 | 0.48 | 0.96 | 22 | 6998 | 3 | 1 | 0 | 2 | 24 | |
| 3O58_2 | 0.79 | 0.76 | 0.83 | 29 | 7225 | 7 | 3 | 3 | 1 | 9 | |
| 3O58_3 | 0.37 | 0.26 | 0.53 | 9 | 12386 | 8 | 2 | 6 | 0 | 26 | |
| 3PDR_A | 0.76 | 0.61 | 0.96 | 44 | 12834 | 3 | 0 | 2 | 1 | 28 | |
| 3RKF_A | 0.68 | 0.50 | 0.94 | 17 | 2193 | 1 | 0 | 1 | 0 | 17 | |
| 3SD1_A | 0.70 | 0.60 | 0.83 | 25 | 3886 | 5 | 1 | 4 | 0 | 17 | |
| 4A1C_3 | 0.74 | 0.57 | 0.97 | 31 | 7108 | 1 | 0 | 1 | 0 | 23 | |
| 4A1C_2 | 0.17 | 0.15 | 0.19 | 5 | 11755 | 23 | 2 | 19 | 2 | 28 | |
| 4AOB_A | 0.72 | 0.52 | 1.00 | 22 | 4349 | 1 | 0 | 0 | 1 | 20 | |
| 4ENB_A | 0.46 | 0.21 | 1.00 | 4 | 1271 | 0 | 0 | 0 | 0 | 15 | |
| 4ENC_A | 0.56 | 0.32 | 1.00 | 6 | 1320 | 0 | 0 | 0 | 0 | 13 |
Performance of HotKnots - scored lower in this pairwise comparison
1. Total counts & total scores for HotKnots
| Total Base Pair Counts | |
|---|---|
| Total TP | 548 |
| Total TN | 209266 |
| Total FP | 355 |
| Total FP CONTRA | 52 |
| Total FP INCONS | 240 |
| Total FP COMP | 63 |
| Total FN | 518 |
| Total Scores | |
|---|---|
| MCC | 0.577 |
| Average MCC ± 95% Confidence Intervals | 0.611 ± 0.095 |
| Sensitivity | 0.514 |
| Positive Predictive Value | 0.652 |
| Nr of predictions | 28 |
2. Individual counts for HotKnots [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| 2KDQ_B | 0.95 | 0.91 | 1.00 | 10 | 396 | 0 | 0 | 0 | 0 | 1 | |
| 2L94_A | 0.97 | 0.95 | 1.00 | 19 | 971 | 0 | 0 | 0 | 0 | 1 | |
| 2WRQ_Y | 0.57 | 0.59 | 0.56 | 10 | 2832 | 13 | 5 | 3 | 5 | 7 | |
| 2XKV_B | 0.51 | 0.50 | 0.53 | 10 | 4541 | 23 | 0 | 9 | 14 | 10 | |
| 2XQD_Y | 0.88 | 0.78 | 1.00 | 21 | 2829 | 0 | 0 | 0 | 0 | 6 | |
| 2XXA_G | 0.34 | 0.31 | 0.39 | 13 | 5118 | 20 | 1 | 19 | 0 | 29 | |
| 3A2K_C | 0.42 | 0.39 | 0.46 | 11 | 2902 | 13 | 2 | 11 | 0 | 17 | |
| 3AMU_B | 0.70 | 0.59 | 0.84 | 16 | 2984 | 5 | 0 | 3 | 2 | 11 | |
| 3G4S_9 | 0.50 | 0.39 | 0.65 | 22 | 7347 | 12 | 1 | 11 | 0 | 35 | |
| 3GX2_A | 0.68 | 0.55 | 0.85 | 22 | 4345 | 5 | 0 | 4 | 1 | 18 | |
| 3IVN_B | 0.78 | 0.61 | 1.00 | 19 | 2327 | 0 | 0 | 0 | 0 | 12 | |
| 3IZ4_A | 0.51 | 0.47 | 0.55 | 62 | 70763 | 52 | 10 | 41 | 1 | 70 | |
| 3IZF_C | 0.70 | 0.61 | 0.80 | 33 | 6862 | 8 | 1 | 7 | 0 | 21 | |
| 3JYV_7 | -0.01 | 0.00 | 0.00 | 0 | 2828 | 22 | 1 | 21 | 0 | 32 | |
| 3JYX_3 | 0.62 | 0.63 | 0.61 | 17 | 6300 | 22 | 1 | 10 | 11 | 10 | |
| 3JYX_4 | 0.32 | 0.30 | 0.33 | 10 | 12216 | 31 | 5 | 15 | 11 | 23 | |
| 3LA5_A | 0.78 | 0.62 | 1.00 | 21 | 2464 | 0 | 0 | 0 | 0 | 13 | |
| 3NPB_A | 0.78 | 0.65 | 0.94 | 30 | 6989 | 5 | 0 | 2 | 3 | 16 | |
| 3O58_2 | 0.71 | 0.71 | 0.71 | 27 | 7222 | 12 | 4 | 7 | 1 | 11 | |
| 3O58_3 | 0.23 | 0.26 | 0.21 | 9 | 12360 | 34 | 10 | 24 | 0 | 26 | |
| 3PDR_A | 0.67 | 0.56 | 0.82 | 40 | 12831 | 11 | 0 | 9 | 2 | 32 | |
| 3RKF_A | 0.76 | 0.59 | 1.00 | 20 | 2191 | 0 | 0 | 0 | 0 | 14 | |
| 3SD1_A | 0.64 | 0.52 | 0.79 | 22 | 3888 | 6 | 1 | 5 | 0 | 20 | |
| 4A1C_3 | 0.70 | 0.59 | 0.82 | 32 | 7101 | 7 | 1 | 6 | 0 | 22 | |
| 4A1C_2 | 0.14 | 0.15 | 0.14 | 5 | 11745 | 42 | 6 | 25 | 11 | 28 | |
| 4AOB_A | 0.50 | 0.40 | 0.63 | 17 | 4344 | 11 | 2 | 8 | 1 | 25 | |
| 4ENB_A | 0.89 | 0.79 | 1.00 | 15 | 1260 | 0 | 0 | 0 | 0 | 4 | |
| 4ENC_A | 0.86 | 0.79 | 0.94 | 15 | 1310 | 1 | 1 | 0 | 0 | 4 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.