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Table of contents:
- Overview
- Performance Plots
- Performance of IPknot - scored higher in this pairwise comparison
- Performance of Afold - scored lower in this pairwise comparison
- Compile and download dataset for IPknot & Afold [.zip] - may take several seconds...
Overview
| Metric | IPknot | Afold | |
|---|---|---|---|
| MCC | 0.728 | > | 0.670 |
| Average MCC ± 95% Confidence Intervals | 0.757 ± 0.111 | > | 0.720 ± 0.134 |
| Sensitivity | 0.628 | > | 0.615 |
| Positive Predictive Value | 0.848 | > | 0.738 |
| Total TP | 279 | > | 273 |
| Total TN | 42809 | > | 42768 |
| Total FP | 62 | < | 123 |
| Total FP CONTRA | 11 | < | 13 |
| Total FP INCONS | 39 | < | 84 |
| Total FP COMP | 12 | < | 26 |
| Total FN | 165 | < | 171 |
| P-value | 5.06544643719e-08 | ||
Performance plots
Performance of IPknot - scored higher in this pairwise comparison
1. Total counts & total scores for IPknot
| Total Base Pair Counts | |
|---|---|
| Total TP | 279 |
| Total TN | 42809 |
| Total FP | 62 |
| Total FP CONTRA | 11 |
| Total FP INCONS | 39 |
| Total FP COMP | 12 |
| Total FN | 165 |
| Total Scores | |
|---|---|
| MCC | 0.728 |
| Average MCC ± 95% Confidence Intervals | 0.757 ± 0.111 |
| Sensitivity | 0.628 |
| Positive Predictive Value | 0.848 |
| Nr of predictions | 24 |
2. Individual counts for IPknot [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| 2LBS_A | - | 1.00 | 1.00 | 1.00 | 14 | 482 | 0 | 0 | 0 | 0 | 0 |
| 2LC8_A | 0.40 | 0.30 | 0.55 | 6 | 1529 | 5 | 1 | 4 | 0 | 14 | |
| 2LDL_A | - | 0.90 | 0.82 | 1.00 | 9 | 342 | 0 | 0 | 0 | 0 | 2 |
| 2LDT_A | - | 0.85 | 0.73 | 1.00 | 11 | 454 | 0 | 0 | 0 | 0 | 4 |
| 2LHP_A | - | 0.97 | 0.94 | 1.00 | 15 | 651 | 0 | 0 | 0 | 0 | 1 |
| 2LI4_A | - | 0.93 | 0.88 | 1.00 | 14 | 482 | 0 | 0 | 0 | 0 | 2 |
| 2LJJ_A | - | 1.00 | 1.00 | 1.00 | 8 | 343 | 2 | 0 | 0 | 2 | 0 |
| 2LK3_A | - | 0.95 | 0.90 | 1.00 | 9 | 267 | 0 | 0 | 0 | 0 | 1 |
| 2LKR_A | - | 0.84 | 0.77 | 0.91 | 30 | 6072 | 4 | 0 | 3 | 1 | 9 |
| 2LQZ_A | - | 0.85 | 0.82 | 0.90 | 9 | 341 | 1 | 1 | 0 | 0 | 2 |
| 2LWK_A | - | 0.83 | 0.77 | 0.91 | 10 | 485 | 1 | 0 | 1 | 0 | 3 |
| 2YIE_Z | - | 0.43 | 0.42 | 0.45 | 5 | 1529 | 6 | 3 | 3 | 0 | 7 |
| 2YIE_X | - | 0.67 | 0.58 | 0.78 | 7 | 1369 | 3 | 1 | 1 | 1 | 5 |
| 3J0L_h | - | 0.78 | 0.60 | 1.00 | 26 | 6079 | 2 | 0 | 0 | 2 | 17 |
| 3J0L_1 | - | 0.76 | 0.63 | 0.92 | 12 | 1212 | 2 | 0 | 1 | 1 | 7 |
| 3J0L_7 | - | -0.01 | 0.00 | 0.00 | 0 | 1218 | 7 | 0 | 7 | 0 | 17 |
| 3RKF_A | 0.76 | 0.59 | 1.00 | 20 | 2191 | 0 | 0 | 0 | 0 | 14 | |
| 3SIU_F | - | 0.73 | 0.55 | 1.00 | 6 | 372 | 0 | 0 | 0 | 0 | 5 |
| 3SN2_B | 0.96 | 0.92 | 1.00 | 11 | 395 | 0 | 0 | 0 | 0 | 1 | |
| 3U4M_B | - | 0.68 | 0.54 | 0.87 | 20 | 3137 | 3 | 1 | 2 | 0 | 17 |
| 3VJR_D | - | 0.96 | 0.92 | 1.00 | 12 | 618 | 0 | 0 | 0 | 0 | 1 |
| 4A1C_2 | 0.17 | 0.15 | 0.19 | 5 | 11755 | 26 | 4 | 17 | 5 | 28 | |
| 4A4U_A | - | 1.00 | 1.00 | 1.00 | 9 | 222 | 0 | 0 | 0 | 0 | 0 |
| 4ENB_A | 0.76 | 0.58 | 1.00 | 11 | 1264 | 0 | 0 | 0 | 0 | 8 |
Performance of Afold - scored lower in this pairwise comparison
1. Total counts & total scores for Afold
| Total Base Pair Counts | |
|---|---|
| Total TP | 273 |
| Total TN | 42768 |
| Total FP | 123 |
| Total FP CONTRA | 13 |
| Total FP INCONS | 84 |
| Total FP COMP | 26 |
| Total FN | 171 |
| Total Scores | |
|---|---|
| MCC | 0.670 |
| Average MCC ± 95% Confidence Intervals | 0.720 ± 0.134 |
| Sensitivity | 0.615 |
| Positive Predictive Value | 0.738 |
| Nr of predictions | 24 |
2. Individual counts for Afold [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| 2LBS_A | - | 1.00 | 1.00 | 1.00 | 14 | 482 | 0 | 0 | 0 | 0 | 0 |
| 2LC8_A | 0.61 | 0.55 | 0.69 | 11 | 1524 | 6 | 0 | 5 | 1 | 9 | |
| 2LDL_A | - | 0.90 | 0.82 | 1.00 | 9 | 342 | 1 | 0 | 0 | 1 | 2 |
| 2LDT_A | - | 0.85 | 0.73 | 1.00 | 11 | 454 | 0 | 0 | 0 | 0 | 4 |
| 2LHP_A | - | 0.97 | 0.94 | 1.00 | 15 | 651 | 0 | 0 | 0 | 0 | 1 |
| 2LI4_A | - | 0.93 | 0.88 | 1.00 | 14 | 482 | 0 | 0 | 0 | 0 | 2 |
| 2LJJ_A | - | 1.00 | 1.00 | 1.00 | 8 | 343 | 2 | 0 | 0 | 2 | 0 |
| 2LK3_A | - | 0.95 | 0.90 | 1.00 | 9 | 267 | 0 | 0 | 0 | 0 | 1 |
| 2LKR_A | - | 0.93 | 0.87 | 1.00 | 34 | 6071 | 3 | 0 | 0 | 3 | 5 |
| 2LQZ_A | - | 0.85 | 0.82 | 0.90 | 9 | 341 | 1 | 1 | 0 | 0 | 2 |
| 2LWK_A | - | 0.75 | 0.69 | 0.82 | 9 | 485 | 2 | 0 | 2 | 0 | 4 |
| 2YIE_Z | - | -0.01 | 0.00 | 0.00 | 0 | 1525 | 16 | 3 | 12 | 1 | 12 |
| 2YIE_X | - | 0.36 | 0.33 | 0.40 | 4 | 1368 | 8 | 2 | 4 | 2 | 8 |
| 3J0L_h | - | 0.73 | 0.60 | 0.90 | 26 | 6076 | 5 | 0 | 3 | 2 | 17 |
| 3J0L_1 | - | 0.73 | 0.63 | 0.86 | 12 | 1211 | 3 | 0 | 2 | 1 | 7 |
| 3J0L_7 | - | -0.01 | 0.00 | 0.00 | 0 | 1210 | 15 | 1 | 14 | 0 | 17 |
| 3RKF_A | 0.76 | 0.59 | 1.00 | 20 | 2191 | 0 | 0 | 0 | 0 | 14 | |
| 3SIU_F | - | 0.85 | 0.73 | 1.00 | 8 | 370 | 0 | 0 | 0 | 0 | 3 |
| 3SN2_B | 0.96 | 0.92 | 1.00 | 11 | 395 | 0 | 0 | 0 | 0 | 1 | |
| 3U4M_B | - | 0.38 | 0.32 | 0.46 | 12 | 3134 | 14 | 0 | 14 | 0 | 25 |
| 3VJR_D | - | 0.96 | 0.92 | 1.00 | 12 | 618 | 1 | 0 | 0 | 1 | 1 |
| 4A1C_2 | 0.14 | 0.15 | 0.14 | 5 | 11745 | 43 | 5 | 26 | 12 | 28 | |
| 4A4U_A | - | 1.00 | 1.00 | 1.00 | 9 | 222 | 0 | 0 | 0 | 0 | 0 |
| 4ENB_A | 0.67 | 0.58 | 0.79 | 11 | 1261 | 3 | 1 | 2 | 0 | 8 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.