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Table of contents:
- Overview
- Performance Plots
- Performance of Alterna - scored higher in this pairwise comparison
- Performance of RNAalifold(seed) - scored lower in this pairwise comparison
- Compile and download dataset for Alterna & RNAalifold(seed) [.zip] - may take several seconds...
Overview
| Metric | Alterna | RNAalifold(seed) | |
|---|---|---|---|
| MCC | 0.763 | > | 0.672 |
| Average MCC ± 95% Confidence Intervals | 0.788 ± 0.098 | > | 0.640 ± 0.137 |
| Sensitivity | 0.683 | > | 0.524 |
| Positive Predictive Value | 0.858 | < | 0.870 |
| Total TP | 314 | > | 241 |
| Total TN | 36840 | < | 36929 |
| Total FP | 69 | > | 41 |
| Total FP CONTRA | 4 | < | 5 |
| Total FP INCONS | 48 | > | 31 |
| Total FP COMP | 17 | > | 5 |
| Total FN | 146 | < | 219 |
| P-value | 2.45805449719e-08 | ||
Performance plots
Performance of Alterna - scored higher in this pairwise comparison
1. Total counts & total scores for Alterna
| Total Base Pair Counts | |
|---|---|
| Total TP | 314 |
| Total TN | 36840 |
| Total FP | 69 |
| Total FP CONTRA | 4 |
| Total FP INCONS | 48 |
| Total FP COMP | 17 |
| Total FN | 146 |
| Total Scores | |
|---|---|
| MCC | 0.763 |
| Average MCC ± 95% Confidence Intervals | 0.788 ± 0.098 |
| Sensitivity | 0.683 |
| Positive Predictive Value | 0.858 |
| Nr of predictions | 18 |
2. Individual counts for Alterna [ 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 | 0.92 | 0.89 | 0.94 | 17 | 1110 | 2 | 0 | 1 | 1 | 2 | |
| 2KUR_A | 0.90 | 0.86 | 0.95 | 18 | 1109 | 1 | 0 | 1 | 0 | 3 | |
| 2KUU_A | 0.87 | 0.81 | 0.94 | 17 | 1110 | 2 | 0 | 1 | 1 | 4 | |
| 2KUV_A | 0.88 | 0.82 | 0.95 | 18 | 1109 | 1 | 0 | 1 | 0 | 4 | |
| 2KUW_A | 0.95 | 0.90 | 1.00 | 19 | 1109 | 0 | 0 | 0 | 0 | 2 | |
| 2KX8_A | 0.88 | 0.83 | 0.94 | 15 | 845 | 1 | 0 | 1 | 0 | 3 | |
| 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 | 0.46 | 0.40 | 0.53 | 8 | 1525 | 7 | 0 | 7 | 0 | 12 | |
| 2XKV_B | 0.45 | 0.45 | 0.45 | 9 | 4540 | 25 | 0 | 11 | 14 | 11 | |
| 3A3A_A | 0.84 | 0.70 | 1.00 | 26 | 3629 | 0 | 0 | 0 | 0 | 11 | |
| 3GX2_A | 0.47 | 0.40 | 0.57 | 16 | 4343 | 13 | 1 | 11 | 1 | 24 | |
| 3IVN_B | 0.74 | 0.61 | 0.90 | 19 | 2325 | 2 | 1 | 1 | 0 | 12 | |
| 3LA5_A | 0.78 | 0.62 | 1.00 | 21 | 2464 | 0 | 0 | 0 | 0 | 13 | |
| 3RKF_A | 0.69 | 0.56 | 0.86 | 19 | 2189 | 3 | 1 | 2 | 0 | 15 | |
| 3SD1_A | 0.46 | 0.38 | 0.57 | 16 | 3888 | 12 | 1 | 11 | 0 | 26 |
Performance of RNAalifold(seed) - scored lower in this pairwise comparison
1. Total counts & total scores for RNAalifold(seed)
| Total Base Pair Counts | |
|---|---|
| Total TP | 241 |
| Total TN | 36929 |
| Total FP | 41 |
| Total FP CONTRA | 5 |
| Total FP INCONS | 31 |
| Total FP COMP | 5 |
| Total FN | 219 |
| Total Scores | |
|---|---|
| MCC | 0.672 |
| Average MCC ± 95% Confidence Intervals | 0.640 ± 0.137 |
| Sensitivity | 0.524 |
| Positive Predictive Value | 0.870 |
| 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 |
| 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 | |
| 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 | |
| 3LA5_A | 0.63 | 0.47 | 0.84 | 16 | 2466 | 3 | 1 | 2 | 0 | 18 | |
| 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 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.