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Table of contents:
- Overview
- Performance Plots
- Performance of CRWrnafold - scored higher in this pairwise comparison
- Performance of Pknots - scored lower in this pairwise comparison
- Compile and download dataset for CRWrnafold & Pknots [.zip] - may take several seconds...
Overview
| Metric | CRWrnafold | Pknots | |
|---|---|---|---|
| MCC | 0.585 | > | 0.545 |
| Average MCC ± 95% Confidence Intervals | 0.639 ± 0.123 | < | 0.641 ± 0.119 |
| Sensitivity | 0.522 | > | 0.498 |
| Positive Predictive Value | 0.663 | > | 0.604 |
| Total TP | 343 | > | 327 |
| Total TN | 69824 | > | 69800 |
| Total FP | 196 | < | 238 |
| Total FP CONTRA | 24 | = | 24 |
| Total FP INCONS | 150 | < | 190 |
| Total FP COMP | 22 | < | 24 |
| Total FN | 314 | < | 330 |
| P-value | 4.83792096436e-08 | ||
Performance plots
Performance of CRWrnafold - scored higher in this pairwise comparison
1. Total counts & total scores for CRWrnafold
| Total Base Pair Counts | |
|---|---|
| Total TP | 343 |
| Total TN | 69824 |
| Total FP | 196 |
| Total FP CONTRA | 24 |
| Total FP INCONS | 150 |
| Total FP COMP | 22 |
| Total FN | 314 |
| Total Scores | |
|---|---|
| MCC | 0.585 |
| Average MCC ± 95% Confidence Intervals | 0.639 ± 0.123 |
| Sensitivity | 0.522 |
| Positive Predictive Value | 0.663 |
| Nr of predictions | 32 |
2. Individual counts for CRWrnafold [ 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 | 1525 | 15 | 2 | 13 | 0 | 20 | |
| 2LDL_A | - | 0.85 | 0.73 | 1.00 | 8 | 343 | 1 | 0 | 0 | 1 | 3 |
| 2LDT_A | - | 0.85 | 0.73 | 1.00 | 11 | 454 | 0 | 0 | 0 | 0 | 4 |
| 2LHP_A | - | 0.93 | 0.88 | 1.00 | 14 | 652 | 0 | 0 | 0 | 0 | 2 |
| 2LI4_A | - | 0.93 | 0.88 | 1.00 | 14 | 482 | 0 | 0 | 0 | 0 | 2 |
| 2LK3_A | - | 0.95 | 0.90 | 1.00 | 9 | 267 | 0 | 0 | 0 | 0 | 1 |
| 2LKR_A | - | 0.52 | 0.44 | 0.63 | 17 | 6078 | 12 | 2 | 8 | 2 | 22 |
| 2LQZ_A | - | 0.85 | 0.82 | 0.90 | 9 | 341 | 1 | 1 | 0 | 0 | 2 |
| 2YIE_Z | - | -0.01 | 0.00 | 0.00 | 0 | 1525 | 15 | 3 | 12 | 0 | 12 |
| 2YIE_X | - | 0.36 | 0.33 | 0.40 | 4 | 1368 | 9 | 2 | 4 | 3 | 8 |
| 3AMU_B | 0.67 | 0.59 | 0.76 | 16 | 2982 | 7 | 0 | 5 | 2 | 11 | |
| 3J0L_7 | - | -0.01 | 0.00 | 0.00 | 0 | 1212 | 13 | 0 | 13 | 0 | 17 |
| 3J0L_g | - | -0.01 | 0.00 | 0.00 | 0 | 461 | 4 | 1 | 3 | 0 | 4 |
| 3J0L_2 | - | 0.25 | 0.24 | 0.28 | 8 | 6187 | 23 | 2 | 19 | 2 | 25 |
| 3J0L_h | - | 0.81 | 0.65 | 1.00 | 28 | 6077 | 0 | 0 | 0 | 0 | 15 |
| 3J0L_a | - | 0.39 | 0.31 | 0.50 | 5 | 1118 | 5 | 1 | 4 | 0 | 11 |
| 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 | 3 | 0 | 1 | 2 | 7 |
| 3J16_L | 0.84 | 0.70 | 1.00 | 21 | 2754 | 0 | 0 | 0 | 0 | 9 | |
| 3SD1_A | 0.52 | 0.45 | 0.61 | 19 | 3885 | 12 | 2 | 10 | 0 | 23 | |
| 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 | - | 1.00 | 1.00 | 1.00 | 6 | 247 | 0 | 0 | 0 | 0 | 0 |
| 3TS2_V | - | 1.00 | 1.00 | 1.00 | 5 | 271 | 0 | 0 | 0 | 0 | 0 |
| 3U4M_B | - | 0.38 | 0.32 | 0.46 | 12 | 3134 | 14 | 0 | 14 | 0 | 25 |
| 4A1C_3 | 0.70 | 0.59 | 0.84 | 32 | 7102 | 6 | 0 | 6 | 0 | 22 | |
| 4A1C_2 | 0.13 | 0.15 | 0.13 | 5 | 11741 | 44 | 4 | 31 | 9 | 28 | |
| 4A4U_A | - | 1.00 | 1.00 | 1.00 | 9 | 222 | 0 | 0 | 0 | 0 | 0 |
| 4AOB_A | 0.59 | 0.48 | 0.74 | 20 | 4344 | 8 | 2 | 5 | 1 | 22 | |
| 4ENB_A | 0.70 | 0.58 | 0.85 | 11 | 1262 | 2 | 1 | 1 | 0 | 8 | |
| 4ENC_A | 0.70 | 0.58 | 0.85 | 11 | 1313 | 2 | 1 | 1 | 0 | 8 |
Performance of Pknots - scored lower in this pairwise comparison
1. Total counts & total scores for Pknots
| Total Base Pair Counts | |
|---|---|
| Total TP | 327 |
| Total TN | 69800 |
| Total FP | 238 |
| Total FP CONTRA | 24 |
| Total FP INCONS | 190 |
| Total FP COMP | 24 |
| Total FN | 330 |
| Total Scores | |
|---|---|
| MCC | 0.545 |
| Average MCC ± 95% Confidence Intervals | 0.641 ± 0.119 |
| Sensitivity | 0.498 |
| Positive Predictive Value | 0.604 |
| Nr of predictions | 32 |
2. Individual counts for Pknots [ 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 | 0.79 | 0.75 | 0.83 | 15 | 1522 | 3 | 1 | 2 | 0 | 5 | |
| 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 |
| 2LK3_A | - | 0.95 | 0.90 | 1.00 | 9 | 267 | 0 | 0 | 0 | 0 | 1 |
| 2LKR_A | - | 0.44 | 0.44 | 0.45 | 17 | 6067 | 22 | 4 | 17 | 1 | 22 |
| 2LQZ_A | - | 0.85 | 0.82 | 0.90 | 9 | 341 | 1 | 1 | 0 | 0 | 2 |
| 2YIE_Z | - | -0.01 | 0.00 | 0.00 | 0 | 1525 | 15 | 3 | 12 | 0 | 12 |
| 2YIE_X | - | 0.36 | 0.33 | 0.40 | 4 | 1368 | 6 | 2 | 4 | 0 | 8 |
| 3AMU_B | 0.86 | 0.74 | 1.00 | 20 | 2983 | 2 | 0 | 0 | 2 | 7 | |
| 3J0L_7 | - | 0.28 | 0.29 | 0.29 | 5 | 1208 | 12 | 0 | 12 | 0 | 12 |
| 3J0L_g | - | -0.01 | 0.00 | 0.00 | 0 | 460 | 5 | 2 | 3 | 0 | 4 |
| 3J0L_2 | - | 0.36 | 0.36 | 0.36 | 12 | 6183 | 23 | 3 | 18 | 2 | 21 |
| 3J0L_h | - | 0.58 | 0.49 | 0.70 | 21 | 6075 | 11 | 0 | 9 | 2 | 22 |
| 3J0L_a | - | 0.35 | 0.31 | 0.42 | 5 | 1116 | 7 | 1 | 6 | 0 | 11 |
| 3J0L_8 | - | 0.93 | 0.88 | 1.00 | 7 | 183 | 0 | 0 | 0 | 0 | 1 |
| 3J0L_1 | - | 0.65 | 0.47 | 0.90 | 9 | 1215 | 2 | 0 | 1 | 1 | 10 |
| 3J16_L | 0.34 | 0.30 | 0.41 | 9 | 2753 | 13 | 0 | 13 | 0 | 21 | |
| 3SD1_A | 0.65 | 0.52 | 0.81 | 22 | 3889 | 5 | 0 | 5 | 0 | 20 | |
| 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 |
| 3U4M_B | - | 0.26 | 0.22 | 0.32 | 8 | 3135 | 17 | 0 | 17 | 0 | 29 |
| 4A1C_3 | 0.25 | 0.22 | 0.29 | 12 | 7099 | 29 | 1 | 28 | 0 | 42 | |
| 4A1C_2 | 0.24 | 0.24 | 0.25 | 8 | 11749 | 36 | 3 | 21 | 12 | 25 | |
| 4A4U_A | - | 1.00 | 1.00 | 1.00 | 9 | 222 | 0 | 0 | 0 | 0 | 0 |
| 4AOB_A | 0.17 | 0.14 | 0.21 | 6 | 4343 | 23 | 1 | 21 | 1 | 36 | |
| 4ENB_A | 0.83 | 0.79 | 0.88 | 15 | 1258 | 2 | 1 | 1 | 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.