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Table of contents:
- Overview
- Performance Plots
- Performance of MXScarna(seed) - scored higher in this pairwise comparison
- Performance of ProbKnot - scored lower in this pairwise comparison
- Compile and download dataset for MXScarna(seed) & ProbKnot [.zip] - may take several seconds...
Overview
| Metric | MXScarna(seed) | ProbKnot | |
|---|---|---|---|
| MCC | 0.653 | > | 0.570 |
| Average MCC ± 95% Confidence Intervals | 0.621 ± 0.097 | > | 0.610 ± 0.108 |
| Sensitivity | 0.541 | > | 0.529 |
| Positive Predictive Value | 0.791 | > | 0.618 |
| Total TP | 558 | > | 546 |
| Total TN | 241610 | > | 241432 |
| Total FP | 202 | < | 395 |
| Total FP CONTRA | 23 | < | 60 |
| Total FP INCONS | 124 | < | 277 |
| Total FP COMP | 55 | < | 58 |
| Total FN | 474 | < | 486 |
| P-value | 5.1503931209e-08 | ||
Performance plots
Performance of MXScarna(seed) - scored higher in this pairwise comparison
1. Total counts & total scores for MXScarna(seed)
| Total Base Pair Counts | |
|---|---|
| Total TP | 558 |
| Total TN | 241610 |
| Total FP | 202 |
| Total FP CONTRA | 23 |
| Total FP INCONS | 124 |
| Total FP COMP | 55 |
| Total FN | 474 |
| Total Scores | |
|---|---|
| MCC | 0.653 |
| Average MCC ± 95% Confidence Intervals | 0.621 ± 0.097 |
| Sensitivity | 0.541 |
| Positive Predictive Value | 0.791 |
| Nr of predictions | 26 |
2. Individual counts for MXScarna(seed) [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| 2KX8_A | -0.01 | 0.00 | 0.00 | 0 | 859 | 2 | 0 | 2 | 0 | 18 | |
| 2L1F_B | 0.96 | 0.92 | 1.00 | 23 | 2122 | 0 | 0 | 0 | 0 | 2 | |
| 2L1F_A | 0.91 | 0.88 | 0.95 | 21 | 2058 | 1 | 0 | 1 | 0 | 3 | |
| 2L94_A | 0.57 | 0.55 | 0.61 | 11 | 972 | 7 | 0 | 7 | 0 | 9 | |
| 2LC8_A | -0.01 | 0.00 | 0.00 | 0 | 1530 | 12 | 0 | 10 | 2 | 20 | |
| 2XKV_B | 0.59 | 0.55 | 0.65 | 11 | 4543 | 18 | 0 | 6 | 12 | 9 | |
| 2XQD_Y | 0.77 | 0.67 | 0.90 | 18 | 2830 | 2 | 0 | 2 | 0 | 9 | |
| 2XXA_G | 0.67 | 0.57 | 0.80 | 24 | 5121 | 7 | 0 | 6 | 1 | 18 | |
| 3AKZ_H | 0.86 | 0.75 | 1.00 | 21 | 2680 | 0 | 0 | 0 | 0 | 7 | |
| 3AMU_B | 0.84 | 0.70 | 1.00 | 19 | 2984 | 1 | 0 | 0 | 1 | 8 | |
| 3IYQ_A | 0.45 | 0.38 | 0.54 | 36 | 60659 | 37 | 4 | 27 | 6 | 58 | |
| 3IZ4_A | 0.69 | 0.55 | 0.88 | 72 | 70794 | 11 | 3 | 7 | 1 | 60 | |
| 3IZF_C | 0.67 | 0.57 | 0.79 | 31 | 6864 | 9 | 1 | 7 | 1 | 23 | |
| 3J16_L | 0.82 | 0.67 | 1.00 | 20 | 2755 | 0 | 0 | 0 | 0 | 10 | |
| 3NPB_A | 0.69 | 0.59 | 0.82 | 27 | 6988 | 9 | 2 | 4 | 3 | 19 | |
| 3O58_3 | 0.45 | 0.34 | 0.60 | 12 | 12383 | 19 | 2 | 6 | 11 | 23 | |
| 3O58_2 | 0.79 | 0.79 | 0.79 | 30 | 7222 | 10 | 4 | 4 | 2 | 8 | |
| 3PDR_A | 0.73 | 0.63 | 0.87 | 45 | 12828 | 9 | 2 | 5 | 2 | 27 | |
| 3RKF_A | 0.72 | 0.53 | 1.00 | 18 | 2193 | 0 | 0 | 0 | 0 | 16 | |
| 3SD1_A | 0.63 | 0.55 | 0.74 | 23 | 3885 | 8 | 1 | 7 | 0 | 19 | |
| 3UZL_B | 0.66 | 0.49 | 0.90 | 18 | 3550 | 2 | 1 | 1 | 0 | 19 | |
| 4A1C_3 | 0.75 | 0.65 | 0.88 | 35 | 7100 | 5 | 1 | 4 | 0 | 19 | |
| 4A1C_2 | 0.35 | 0.24 | 0.50 | 8 | 11765 | 20 | 1 | 7 | 12 | 25 | |
| 4AOB_A | 0.66 | 0.55 | 0.79 | 23 | 4342 | 7 | 0 | 6 | 1 | 19 | |
| 4ENB_A | 0.48 | 0.32 | 0.75 | 6 | 1267 | 2 | 0 | 2 | 0 | 13 | |
| 4ENC_A | 0.43 | 0.32 | 0.60 | 6 | 1316 | 4 | 1 | 3 | 0 | 13 |
Performance of ProbKnot - scored lower in this pairwise comparison
1. Total counts & total scores for ProbKnot
| Total Base Pair Counts | |
|---|---|
| Total TP | 546 |
| Total TN | 241432 |
| Total FP | 395 |
| Total FP CONTRA | 60 |
| Total FP INCONS | 277 |
| Total FP COMP | 58 |
| Total FN | 486 |
| Total Scores | |
|---|---|
| MCC | 0.570 |
| Average MCC ± 95% Confidence Intervals | 0.610 ± 0.108 |
| Sensitivity | 0.529 |
| Positive Predictive Value | 0.618 |
| Nr of predictions | 26 |
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 | |
| 2XQD_Y | 0.90 | 0.81 | 1.00 | 22 | 2828 | 1 | 0 | 0 | 1 | 5 | |
| 2XXA_G | 0.26 | 0.24 | 0.29 | 10 | 5116 | 25 | 1 | 24 | 0 | 32 | |
| 3AKZ_H | 0.73 | 0.75 | 0.72 | 21 | 2672 | 8 | 4 | 4 | 0 | 7 | |
| 3AMU_B | 0.65 | 0.59 | 0.73 | 16 | 2981 | 8 | 0 | 6 | 2 | 11 | |
| 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 | |
| 3IZF_C | 0.72 | 0.61 | 0.85 | 33 | 6864 | 6 | 0 | 6 | 0 | 21 | |
| 3J16_L | 0.35 | 0.33 | 0.38 | 10 | 2749 | 16 | 1 | 15 | 0 | 20 | |
| 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 | |
| 3O58_2 | 0.76 | 0.76 | 0.76 | 29 | 7222 | 10 | 3 | 6 | 1 | 9 | |
| 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 | |
| 3UZL_B | 0.73 | 0.62 | 0.85 | 23 | 3543 | 4 | 0 | 4 | 0 | 14 | |
| 4A1C_3 | 0.73 | 0.61 | 0.87 | 33 | 7102 | 6 | 1 | 4 | 1 | 21 | |
| 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 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.