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Table of contents:
- Overview
- Performance Plots
- Performance of IPknot - scored higher in this pairwise comparison
- Performance of RDfolder - scored lower in this pairwise comparison
- Compile and download dataset for IPknot & RDfolder [.zip] - may take several seconds...
Overview
| Metric | IPknot | RDfolder | |
|---|---|---|---|
| MCC | 0.659 | > | 0.496 |
| Average MCC ± 95% Confidence Intervals | 0.689 ± 0.125 | > | 0.560 ± 0.150 |
| Sensitivity | 0.550 | > | 0.388 |
| Positive Predictive Value | 0.799 | > | 0.647 |
| Total TP | 231 | > | 163 |
| Total TN | 30621 | < | 30658 |
| Total FP | 65 | < | 93 |
| Total FP CONTRA | 8 | < | 11 |
| Total FP INCONS | 50 | < | 78 |
| Total FP COMP | 7 | > | 4 |
| Total FN | 189 | < | 257 |
| P-value | 5.10776592382e-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 | 231 |
| Total TN | 30621 |
| Total FP | 65 |
| Total FP CONTRA | 8 |
| Total FP INCONS | 50 |
| Total FP COMP | 7 |
| Total FN | 189 |
| Total Scores | |
|---|---|
| MCC | 0.659 |
| Average MCC ± 95% Confidence Intervals | 0.689 ± 0.125 |
| Sensitivity | 0.550 |
| Positive Predictive Value | 0.799 |
| Nr of predictions | 25 |
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 |
| 2LK3_A | - | 0.95 | 0.90 | 1.00 | 9 | 267 | 0 | 0 | 0 | 0 | 1 |
| 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 |
| 3AMU_B | 0.70 | 0.59 | 0.84 | 16 | 2984 | 5 | 0 | 3 | 2 | 11 | |
| 3J0L_a | - | 0.21 | 0.19 | 0.25 | 3 | 1116 | 9 | 1 | 8 | 0 | 13 |
| 3J0L_8 | - | 0.93 | 0.88 | 1.00 | 7 | 183 | 0 | 0 | 0 | 0 | 1 |
| 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 |
| 3J0L_g | - | -0.01 | 0.00 | 0.00 | 0 | 461 | 4 | 1 | 3 | 0 | 4 |
| 3J16_L | 0.75 | 0.57 | 1.00 | 17 | 2758 | 0 | 0 | 0 | 0 | 13 | |
| 3RKF_A | 0.76 | 0.59 | 1.00 | 20 | 2191 | 0 | 0 | 0 | 0 | 14 | |
| 3SD1_A | 0.61 | 0.48 | 0.80 | 20 | 3891 | 5 | 0 | 5 | 0 | 22 | |
| 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 | |
| 3TRZ_Z | - | 0.91 | 0.83 | 1.00 | 5 | 205 | 1 | 0 | 0 | 1 | 1 |
| 3TS0_U | - | 1.00 | 1.00 | 1.00 | 6 | 247 | 1 | 0 | 0 | 1 | 0 |
| 3TS2_V | - | 1.00 | 1.00 | 1.00 | 5 | 271 | 0 | 0 | 0 | 0 | 0 |
| 4A4U_A | - | 1.00 | 1.00 | 1.00 | 9 | 222 | 0 | 0 | 0 | 0 | 0 |
| 4AOB_A | 0.42 | 0.33 | 0.54 | 14 | 4345 | 13 | 1 | 11 | 1 | 28 | |
| 4ENB_A | 0.76 | 0.58 | 1.00 | 11 | 1264 | 0 | 0 | 0 | 0 | 8 | |
| 4ENC_A | 0.52 | 0.42 | 0.67 | 8 | 1314 | 4 | 0 | 4 | 0 | 11 |
Performance of RDfolder - scored lower in this pairwise comparison
1. Total counts & total scores for RDfolder
| Total Base Pair Counts | |
|---|---|
| Total TP | 163 |
| Total TN | 30658 |
| Total FP | 93 |
| Total FP CONTRA | 11 |
| Total FP INCONS | 78 |
| Total FP COMP | 4 |
| Total FN | 257 |
| Total Scores | |
|---|---|
| MCC | 0.496 |
| Average MCC ± 95% Confidence Intervals | 0.560 ± 0.150 |
| Sensitivity | 0.388 |
| Positive Predictive Value | 0.647 |
| Nr of predictions | 25 |
2. Individual counts for RDfolder [ 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 | -0.01 | 0.00 | 0.00 | 0 | 1526 | 14 | 2 | 12 | 0 | 20 | |
| 2LDL_A | - | 0.90 | 0.82 | 1.00 | 9 | 342 | 0 | 0 | 0 | 0 | 2 |
| 2LDT_A | - | 0.68 | 0.47 | 1.00 | 7 | 458 | 0 | 0 | 0 | 0 | 8 |
| 2LK3_A | - | 0.95 | 0.90 | 1.00 | 9 | 267 | 0 | 0 | 0 | 0 | 1 |
| 2YIE_Z | - | 0.43 | 0.42 | 0.45 | 5 | 1529 | 6 | 3 | 3 | 0 | 7 |
| 2YIE_X | - | 0.38 | 0.33 | 0.44 | 4 | 1369 | 5 | 1 | 4 | 0 | 8 |
| 3AMU_B | 0.18 | 0.15 | 0.22 | 4 | 2985 | 16 | 2 | 12 | 2 | 23 | |
| 3J0L_a | - | -0.01 | 0.00 | 0.00 | 0 | 1124 | 4 | 1 | 3 | 0 | 16 |
| 3J0L_8 | - | 0.86 | 0.75 | 1.00 | 6 | 184 | 0 | 0 | 0 | 0 | 2 |
| 3J0L_1 | - | 0.65 | 0.47 | 0.90 | 9 | 1215 | 2 | 0 | 1 | 1 | 10 |
| 3J0L_7 | - | -0.01 | 0.00 | 0.00 | 0 | 1220 | 5 | 0 | 5 | 0 | 17 |
| 3J0L_g | - | -0.01 | 0.00 | 0.00 | 0 | 462 | 3 | 1 | 2 | 0 | 4 |
| 3J16_L | 0.22 | 0.17 | 0.31 | 5 | 2759 | 11 | 0 | 11 | 0 | 25 | |
| 3RKF_A | 0.76 | 0.59 | 1.00 | 20 | 2191 | 0 | 0 | 0 | 0 | 14 | |
| 3SD1_A | 0.30 | 0.17 | 0.54 | 7 | 3903 | 6 | 0 | 6 | 0 | 35 | |
| 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 | |
| 3TRZ_Z | - | 0.91 | 0.83 | 1.00 | 5 | 205 | 0 | 0 | 0 | 0 | 1 |
| 3TS0_U | - | 0.91 | 0.83 | 1.00 | 5 | 248 | 0 | 0 | 0 | 0 | 1 |
| 3TS2_V | - | 1.00 | 1.00 | 1.00 | 5 | 271 | 0 | 0 | 0 | 0 | 0 |
| 4A4U_A | - | 1.00 | 1.00 | 1.00 | 9 | 222 | 0 | 0 | 0 | 0 | 0 |
| 4AOB_A | 0.35 | 0.26 | 0.48 | 11 | 4348 | 13 | 1 | 11 | 1 | 31 | |
| 4ENB_A | 0.43 | 0.32 | 0.60 | 6 | 1265 | 4 | 0 | 4 | 0 | 13 | |
| 4ENC_A | 0.43 | 0.32 | 0.60 | 6 | 1316 | 4 | 0 | 4 | 0 | 13 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.