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Table of contents:
- Overview
- Performance Plots
- Performance of RNAalifold(seed) - scored higher in this pairwise comparison
- Performance of Pknots - scored lower in this pairwise comparison
- Compile and download dataset for RNAalifold(seed) & Pknots [.zip] - may take several seconds...
Overview
| Metric | RNAalifold(seed) | Pknots | |
|---|---|---|---|
| MCC | 0.636 | > | 0.636 |
| Average MCC ± 95% Confidence Intervals | 0.612 ± 0.093 | < | 0.705 ± 0.113 |
| Sensitivity | 0.449 | < | 0.588 |
| Positive Predictive Value | 0.905 | > | 0.693 |
| Total TP | 360 | < | 471 |
| Total TN | 105262 | > | 104980 |
| Total FP | 50 | < | 251 |
| Total FP CONTRA | 6 | < | 35 |
| Total FP INCONS | 32 | < | 174 |
| Total FP COMP | 12 | < | 42 |
| Total FN | 441 | > | 330 |
| P-value | 0.475054585957 | ||
Performance plots
Performance of RNAalifold(seed) - scored higher in this pairwise comparison
1. Total counts & total scores for RNAalifold(seed)
| Total Base Pair Counts | |
|---|---|
| Total TP | 360 |
| Total TN | 105262 |
| Total FP | 50 |
| Total FP CONTRA | 6 |
| Total FP INCONS | 32 |
| Total FP COMP | 12 |
| Total FN | 441 |
| Total Scores | |
|---|---|
| MCC | 0.636 |
| Average MCC ± 95% Confidence Intervals | 0.612 ± 0.093 |
| Sensitivity | 0.449 |
| Positive Predictive Value | 0.905 |
| Nr of predictions | 27 |
2. Individual counts for RNAalifold(seed) [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| 2KDQ_B | 0.52 | 0.27 | 1.00 | 3 | 403 | 0 | 0 | 0 | 0 | 8 | |
| 2KE6_A | 0.97 | 0.95 | 1.00 | 18 | 1110 | 1 | 0 | 0 | 1 | 1 | |
| 2KUR_A | 0.95 | 0.90 | 1.00 | 19 | 1109 | 0 | 0 | 0 | 0 | 2 | |
| 2KUU_A | 0.92 | 0.86 | 1.00 | 18 | 1110 | 1 | 0 | 0 | 1 | 3 | |
| 2KUV_A | 0.93 | 0.86 | 1.00 | 19 | 1109 | 0 | 0 | 0 | 0 | 3 | |
| 2KUW_A | 0.84 | 0.76 | 0.94 | 16 | 1111 | 1 | 0 | 1 | 0 | 5 | |
| 2KX8_A | 0.00 | 0.00 | 0.00 | 0 | 861 | 0 | 0 | 0 | 0 | 18 | |
| 2L1F_B | 0.64 | 0.56 | 0.74 | 14 | 2126 | 5 | 0 | 5 | 0 | 11 | |
| 2L1F_A | 0.67 | 0.58 | 0.78 | 14 | 2062 | 4 | 0 | 4 | 0 | 10 | |
| 2L94_A | 0.59 | 0.40 | 0.89 | 8 | 981 | 1 | 0 | 1 | 0 | 12 | |
| 2LC8_A | -0.01 | 0.00 | 0.00 | 0 | 1528 | 12 | 0 | 12 | 0 | 20 | |
| 2XKV_B | 0.59 | 0.35 | 1.00 | 7 | 4553 | 2 | 0 | 0 | 2 | 13 | |
| 2XXA_G | 0.46 | 0.21 | 1.00 | 9 | 5142 | 0 | 0 | 0 | 0 | 33 | |
| 3A3A_A | 0.71 | 0.51 | 1.00 | 19 | 3636 | 0 | 0 | 0 | 0 | 18 | |
| 3GX2_A | 0.74 | 0.55 | 1.00 | 22 | 4349 | 1 | 0 | 0 | 1 | 18 | |
| 3IVN_B | 0.61 | 0.48 | 0.79 | 15 | 2327 | 4 | 2 | 2 | 0 | 16 | |
| 3JYX_4 | 0.46 | 0.21 | 1.00 | 7 | 12239 | 2 | 0 | 0 | 2 | 26 | |
| 3LA5_A | 0.63 | 0.47 | 0.84 | 16 | 2466 | 3 | 1 | 2 | 0 | 18 | |
| 3NPB_A | 0.66 | 0.48 | 0.92 | 22 | 6997 | 3 | 1 | 1 | 1 | 24 | |
| 3O58_3 | 0.51 | 0.26 | 1.00 | 9 | 12394 | 0 | 0 | 0 | 0 | 26 | |
| 3PDR_A | 0.68 | 0.46 | 1.00 | 33 | 12847 | 1 | 0 | 0 | 1 | 39 | |
| 3RKF_A | 0.63 | 0.47 | 0.84 | 16 | 2192 | 3 | 1 | 2 | 0 | 18 | |
| 3SD1_A | 0.58 | 0.40 | 0.85 | 17 | 3896 | 3 | 1 | 2 | 0 | 25 | |
| 4A1C_2 | 0.39 | 0.15 | 1.00 | 5 | 11776 | 2 | 0 | 0 | 2 | 28 | |
| 4AOB_A | 0.72 | 0.52 | 1.00 | 22 | 4349 | 1 | 0 | 0 | 1 | 20 | |
| 4ENB_A | 0.56 | 0.32 | 1.00 | 6 | 1269 | 0 | 0 | 0 | 0 | 13 | |
| 4ENC_A | 0.56 | 0.32 | 1.00 | 6 | 1320 | 0 | 0 | 0 | 0 | 13 |
Performance of Pknots - scored lower in this pairwise comparison
1. Total counts & total scores for Pknots
| Total Base Pair Counts | |
|---|---|
| Total TP | 471 |
| Total TN | 104980 |
| Total FP | 251 |
| Total FP CONTRA | 35 |
| Total FP INCONS | 174 |
| Total FP COMP | 42 |
| Total FN | 330 |
| Total Scores | |
|---|---|
| MCC | 0.636 |
| Average MCC ± 95% Confidence Intervals | 0.705 ± 0.113 |
| Sensitivity | 0.588 |
| Positive Predictive Value | 0.693 |
| Nr of predictions | 27 |
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 |
| 2KDQ_B | 0.95 | 0.91 | 1.00 | 10 | 396 | 0 | 0 | 0 | 0 | 1 | |
| 2KE6_A | 0.97 | 0.95 | 1.00 | 18 | 1110 | 1 | 0 | 0 | 1 | 1 | |
| 2KUR_A | 0.95 | 0.90 | 1.00 | 19 | 1109 | 0 | 0 | 0 | 0 | 2 | |
| 2KUU_A | 0.92 | 0.86 | 1.00 | 18 | 1110 | 1 | 0 | 0 | 1 | 3 | |
| 2KUV_A | 0.93 | 0.86 | 1.00 | 19 | 1109 | 0 | 0 | 0 | 0 | 3 | |
| 2KUW_A | 0.95 | 0.90 | 1.00 | 19 | 1109 | 0 | 0 | 0 | 0 | 2 | |
| 2KX8_A | 0.94 | 0.89 | 1.00 | 16 | 845 | 0 | 0 | 0 | 0 | 2 | |
| 2L1F_B | 0.98 | 0.96 | 1.00 | 24 | 2121 | 0 | 0 | 0 | 0 | 1 | |
| 2L1F_A | 0.98 | 0.96 | 1.00 | 23 | 2057 | 0 | 0 | 0 | 0 | 1 | |
| 2L94_A | 0.92 | 0.90 | 0.95 | 18 | 971 | 1 | 0 | 1 | 0 | 2 | |
| 2LC8_A | 0.79 | 0.75 | 0.83 | 15 | 1522 | 3 | 1 | 2 | 0 | 5 | |
| 2XKV_B | 0.23 | 0.25 | 0.22 | 5 | 4537 | 31 | 1 | 17 | 13 | 15 | |
| 2XXA_G | 0.32 | 0.31 | 0.34 | 13 | 5113 | 25 | 1 | 24 | 0 | 29 | |
| 3A3A_A | 0.87 | 0.76 | 1.00 | 28 | 3627 | 0 | 0 | 0 | 0 | 9 | |
| 3GX2_A | 0.47 | 0.40 | 0.55 | 16 | 4342 | 14 | 1 | 12 | 1 | 24 | |
| 3IVN_B | 0.78 | 0.65 | 0.95 | 20 | 2325 | 1 | 0 | 1 | 0 | 11 | |
| 3JYX_4 | 0.18 | 0.21 | 0.16 | 7 | 12203 | 41 | 13 | 23 | 5 | 26 | |
| 3LA5_A | 0.80 | 0.65 | 1.00 | 22 | 2463 | 0 | 0 | 0 | 0 | 12 | |
| 3NPB_A | 0.76 | 0.67 | 0.86 | 31 | 6985 | 8 | 1 | 4 | 3 | 15 | |
| 3O58_3 | 0.27 | 0.31 | 0.24 | 11 | 12357 | 38 | 11 | 24 | 3 | 24 | |
| 3PDR_A | 0.54 | 0.44 | 0.65 | 32 | 12831 | 19 | 0 | 17 | 2 | 40 | |
| 3RKF_A | 0.77 | 0.62 | 0.95 | 21 | 2189 | 1 | 0 | 1 | 0 | 13 | |
| 3SD1_A | 0.65 | 0.52 | 0.81 | 22 | 3889 | 5 | 0 | 5 | 0 | 20 | |
| 4A1C_2 | 0.24 | 0.24 | 0.25 | 8 | 11749 | 36 | 3 | 21 | 12 | 25 | |
| 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.