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Table of contents:
- Overview
- Performance Plots
- Performance of ProbKnot - scored higher in this pairwise comparison
- Performance of RNAalifold(seed) - scored lower in this pairwise comparison
- Compile and download dataset for ProbKnot & RNAalifold(seed) [.zip] - may take several seconds...
Overview
| Metric | ProbKnot | RNAalifold(seed) | |
|---|---|---|---|
| MCC | 0.520 | > | 0.519 |
| Average MCC ± 95% Confidence Intervals | 0.572 ± 0.150 | > | 0.502 ± 0.104 |
| Sensitivity | 0.487 | > | 0.320 |
| Positive Predictive Value | 0.559 | < | 0.843 |
| Total TP | 359 | > | 236 |
| Total TN | 205471 | < | 205833 |
| Total FP | 336 | > | 55 |
| Total FP CONTRA | 51 | > | 9 |
| Total FP INCONS | 232 | > | 35 |
| Total FP COMP | 53 | > | 11 |
| Total FN | 378 | < | 501 |
| P-value | 0.486848903635 | ||
Performance plots
Performance of ProbKnot - scored higher in this pairwise comparison
1. Total counts & total scores for ProbKnot
| Total Base Pair Counts | |
|---|---|
| Total TP | 359 |
| Total TN | 205471 |
| Total FP | 336 |
| Total FP CONTRA | 51 |
| Total FP INCONS | 232 |
| Total FP COMP | 53 |
| Total FN | 378 |
| Total Scores | |
|---|---|
| MCC | 0.520 |
| Average MCC ± 95% Confidence Intervals | 0.572 ± 0.150 |
| Sensitivity | 0.487 |
| Positive Predictive Value | 0.559 |
| Nr of predictions | 18 |
2. Individual counts for ProbKnot [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| 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 | 0.97 | 0.95 | 1.00 | 19 | 971 | 0 | 0 | 0 | 0 | 1 | |
| 2LC8_A | -0.01 | 0.00 | 0.00 | 0 | 1525 | 15 | 2 | 13 | 0 | 20 | |
| 2XKV_B | 0.51 | 0.50 | 0.53 | 10 | 4541 | 24 | 0 | 9 | 15 | 10 | |
| 2XXA_G | 0.26 | 0.24 | 0.29 | 10 | 5116 | 25 | 1 | 24 | 0 | 32 | |
| 3IYQ_A | 0.28 | 0.31 | 0.26 | 29 | 60616 | 85 | 22 | 59 | 4 | 65 | |
| 3IZ4_A | 0.52 | 0.46 | 0.60 | 61 | 70774 | 46 | 6 | 35 | 5 | 71 | |
| 3NPB_A | 0.72 | 0.61 | 0.85 | 28 | 6988 | 8 | 1 | 4 | 3 | 18 | |
| 3O58_3 | 0.31 | 0.34 | 0.29 | 12 | 12362 | 41 | 4 | 25 | 12 | 23 | |
| 3PDR_A | 0.74 | 0.64 | 0.85 | 46 | 12826 | 10 | 1 | 7 | 2 | 26 | |
| 3RKF_A | 0.73 | 0.59 | 0.91 | 20 | 2189 | 2 | 1 | 1 | 0 | 14 | |
| 3SD1_A | 0.55 | 0.48 | 0.65 | 20 | 3885 | 11 | 2 | 9 | 0 | 22 | |
| 4A1C_2 | 0.13 | 0.15 | 0.12 | 5 | 11738 | 49 | 7 | 31 | 11 | 28 | |
| 4AOB_A | 0.50 | 0.40 | 0.63 | 17 | 4344 | 11 | 2 | 8 | 1 | 25 | |
| 4ENB_A | 0.73 | 0.58 | 0.92 | 11 | 1263 | 1 | 1 | 0 | 0 | 8 | |
| 4ENC_A | 0.45 | 0.42 | 0.50 | 8 | 1310 | 8 | 1 | 7 | 0 | 11 |
Performance of RNAalifold(seed) - scored lower in this pairwise comparison
1. Total counts & total scores for RNAalifold(seed)
| Total Base Pair Counts | |
|---|---|
| Total TP | 236 |
| Total TN | 205833 |
| Total FP | 55 |
| Total FP CONTRA | 9 |
| Total FP INCONS | 35 |
| Total FP COMP | 11 |
| Total FN | 501 |
| Total Scores | |
|---|---|
| MCC | 0.519 |
| Average MCC ± 95% Confidence Intervals | 0.502 ± 0.104 |
| Sensitivity | 0.320 |
| Positive Predictive Value | 0.843 |
| Nr of predictions | 18 |
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 |
| 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 | |
| 3IYQ_A | 0.38 | 0.21 | 0.69 | 20 | 60697 | 13 | 5 | 4 | 4 | 74 | |
| 3IZ4_A | 0.42 | 0.21 | 0.85 | 28 | 70843 | 5 | 1 | 4 | 0 | 104 | |
| 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 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.