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Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison
- Performance of RNASampler(seed) - scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(20) & RNASampler(seed) [.zip] - may take several seconds...
Overview
| Metric | PETfold_pre2.0(20) | RNASampler(seed) | |
|---|---|---|---|
| MCC | 0.735 | > | 0.571 |
| Average MCC ± 95% Confidence Intervals | 0.620 ± 0.146 | > | 0.424 ± 0.109 |
| Sensitivity | 0.627 | > | 0.343 |
| Positive Predictive Value | 0.867 | < | 0.957 |
| Total TP | 411 | > | 225 |
| Total TN | 64185 | < | 64424 |
| Total FP | 94 | > | 25 |
| Total FP CONTRA | 0 | = | 0 |
| Total FP INCONS | 63 | > | 10 |
| Total FP COMP | 31 | > | 15 |
| Total FN | 245 | < | 431 |
| P-value | 3.56938820447e-08 | ||
Performance plots
-
Comparison of performance of PETfold_pre2.0(20) and RNASampler(seed). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for PETfold_pre2.0(20) and RNASampler(seed)).
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Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for PETfold_pre2.0(20) and RNASampler(seed)).
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Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and RNASampler(seed). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for PETfold_pre2.0(20) and RNASampler(seed)).
Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison
1. Total counts & total scores for PETfold_pre2.0(20)
| Total Base Pair Counts | |
|---|---|
| Total TP | 411 |
| Total TN | 64185 |
| Total FP | 94 |
| Total FP CONTRA | 0 |
| Total FP INCONS | 63 |
| Total FP COMP | 31 |
| Total FN | 245 |
| Total Scores | |
|---|---|
| MCC | 0.735 |
| Average MCC ± 95% Confidence Intervals | 0.620 ± 0.146 |
| Sensitivity | 0.627 |
| Positive Predictive Value | 0.867 |
| Nr of predictions | 42 |
2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| PDB_00012 | 1.00 | 1.00 | 1.00 | 7 | 399 | 2 | 0 | 0 | 2 | 0 | |
| PDB_00213 | 0.85 | 0.73 | 1.00 | 30 | 5020 | 0 | 0 | 0 | 0 | 11 | |
| PDB_00553 | 1.00 | 1.00 | 1.00 | 11 | 454 | 0 | 0 | 0 | 0 | 0 | |
| PDB_00810 | 0.84 | 0.71 | 1.00 | 12 | 1069 | 0 | 0 | 0 | 0 | 5 | |
| PDB_01050 | 0.78 | 0.62 | 1.00 | 8 | 622 | 2 | 0 | 0 | 2 | 5 | |
| PDB_01152 | 0.80 | 0.71 | 0.91 | 10 | 550 | 1 | 0 | 1 | 0 | 4 | |
| RFA_00390 | 0.97 | 0.93 | 1.00 | 14 | 1417 | 2 | 0 | 0 | 2 | 1 | |
| RFA_00416 | 0.97 | 0.93 | 1.00 | 14 | 1471 | 2 | 0 | 0 | 2 | 1 | |
| RFA_00433 | 1.00 | 1.00 | 1.00 | 15 | 1416 | 2 | 0 | 0 | 2 | 0 | |
| RFA_00587 | 0.93 | 0.93 | 0.93 | 14 | 4836 | 9 | 0 | 1 | 8 | 1 | |
| RFA_00658 | 0.00 | 0.00 | 0.00 | 0 | 1126 | 3 | 0 | 2 | 1 | 14 | |
| RFA_00664 | -0.01 | 0.00 | 0.00 | 0 | 986 | 4 | 0 | 4 | 0 | 14 | |
| RFA_00667 | -0.01 | 0.00 | 0.00 | 0 | 985 | 5 | 0 | 5 | 0 | 14 | |
| RFA_00668 | -0.01 | 0.00 | 0.00 | 0 | 986 | 4 | 0 | 4 | 0 | 14 | |
| RFA_00672 | -0.01 | 0.00 | 0.00 | 0 | 898 | 5 | 0 | 5 | 0 | 13 | |
| RFA_00673 | -0.01 | 0.00 | 0.00 | 0 | 1123 | 5 | 0 | 5 | 0 | 14 | |
| RFA_00674 | -0.01 | 0.00 | 0.00 | 0 | 1124 | 4 | 0 | 4 | 0 | 14 | |
| RFA_00675 | -0.01 | 0.00 | 0.00 | 0 | 985 | 5 | 0 | 5 | 0 | 14 | |
| RFA_00677 | -0.01 | 0.00 | 0.00 | 0 | 984 | 6 | 0 | 6 | 0 | 14 | |
| RFA_00678 | -0.01 | 0.00 | 0.00 | 0 | 941 | 5 | 0 | 5 | 0 | 14 | |
| RFA_00680 | 0.15 | 0.07 | 0.33 | 1 | 1125 | 3 | 0 | 2 | 1 | 13 | |
| RFA_00704 | -0.01 | 0.00 | 0.00 | 0 | 988 | 3 | 0 | 2 | 1 | 14 | |
| RFA_00707 | -0.01 | 0.00 | 0.00 | 0 | 1029 | 6 | 0 | 6 | 0 | 14 | |
| RFA_00715 | -0.01 | 0.00 | 0.00 | 0 | 942 | 4 | 0 | 4 | 0 | 14 | |
| RFA_00717 | 0.00 | 0.00 | 0.00 | 0 | 902 | 1 | 0 | 1 | 0 | 14 | |
| RFA_00730 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00731 | 1.00 | 1.00 | 1.00 | 12 | 891 | 0 | 0 | 0 | 0 | 0 | |
| RFA_00733 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00734 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00736 | 1.00 | 1.00 | 1.00 | 12 | 891 | 0 | 0 | 0 | 0 | 0 | |
| RFA_00737 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00745 | 1.00 | 1.00 | 1.00 | 12 | 934 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00749 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00758 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00762 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00763 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00764 | 1.00 | 1.00 | 1.00 | 12 | 891 | 1 | 0 | 0 | 1 | 0 | |
| RFA_00765 | 1.00 | 1.00 | 1.00 | 12 | 891 | 0 | 0 | 0 | 0 | 0 | |
| RFA_00786 | 0.97 | 0.94 | 1.00 | 30 | 5020 | 0 | 0 | 0 | 0 | 2 | |
| RFA_00791 | 0.97 | 0.94 | 1.00 | 30 | 5121 | 0 | 0 | 0 | 0 | 2 | |
| RFA_00792 | 0.94 | 0.91 | 0.97 | 29 | 5020 | 1 | 0 | 1 | 0 | 3 | |
| RFA_00801 | 0.97 | 0.94 | 1.00 | 30 | 5020 | 0 | 0 | 0 | 0 | 2 |
Performance of RNASampler(seed) - scored lower in this pairwise comparison
1. Total counts & total scores for RNASampler(seed)
| Total Base Pair Counts | |
|---|---|
| Total TP | 225 |
| Total TN | 64424 |
| Total FP | 25 |
| Total FP CONTRA | 0 |
| Total FP INCONS | 10 |
| Total FP COMP | 15 |
| Total FN | 431 |
| Total Scores | |
|---|---|
| MCC | 0.571 |
| Average MCC ± 95% Confidence Intervals | 0.424 ± 0.109 |
| Sensitivity | 0.343 |
| Positive Predictive Value | 0.957 |
| Nr of predictions | 42 |
2. Individual counts for RNASampler(seed) [ download as .csv ]
| RNA Chain | Rfam family | MCC | SENS | PPV | TP | TN | FP | FP CONTRA | FP INCONS | FP COMP | FN |
| PDB_00012 | 1.00 | 1.00 | 1.00 | 7 | 399 | 3 | 0 | 0 | 3 | 0 | |
| PDB_00213 | 0.76 | 0.59 | 1.00 | 24 | 5026 | 0 | 0 | 0 | 0 | 17 | |
| PDB_00553 | 1.00 | 1.00 | 1.00 | 11 | 454 | 0 | 0 | 0 | 0 | 0 | |
| PDB_00810 | 0.42 | 0.18 | 1.00 | 3 | 1078 | 0 | 0 | 0 | 0 | 14 | |
| PDB_01050 | 0.92 | 0.85 | 1.00 | 11 | 619 | 2 | 0 | 0 | 2 | 2 | |
| PDB_01152 | 0.84 | 0.71 | 1.00 | 10 | 551 | 0 | 0 | 0 | 0 | 4 | |
| RFA_00390 | 0.00 | 0.00 | 0.00 | 0 | 1431 | 0 | 0 | 0 | 0 | 15 | |
| RFA_00416 | 0.63 | 0.40 | 1.00 | 6 | 1479 | 1 | 0 | 0 | 1 | 9 | |
| RFA_00433 | 0.63 | 0.40 | 1.00 | 6 | 1425 | 1 | 0 | 0 | 1 | 9 | |
| RFA_00587 | 1.00 | 1.00 | 1.00 | 15 | 4836 | 5 | 0 | 0 | 5 | 0 | |
| RFA_00658 | 0.00 | 0.00 | 0.00 | 0 | 1128 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00664 | 0.00 | 0.00 | 0.00 | 0 | 990 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00667 | 0.53 | 0.29 | 1.00 | 4 | 986 | 0 | 0 | 0 | 0 | 10 | |
| RFA_00668 | 0.00 | 0.00 | 0.00 | 0 | 990 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00672 | 0.00 | 0.00 | 0.00 | 0 | 903 | 0 | 0 | 0 | 0 | 13 | |
| RFA_00673 | 0.00 | 0.00 | 0.00 | 0 | 1128 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00674 | 0.00 | 0.00 | 0.00 | 0 | 1128 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00675 | 0.00 | 0.00 | 0.00 | 0 | 990 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00677 | 0.00 | 0.00 | 0.00 | 0 | 990 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00678 | 0.00 | 0.00 | 0.00 | 0 | 946 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00680 | 0.00 | 0.00 | 0.00 | 0 | 1128 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00704 | -0.01 | 0.00 | 0.00 | 0 | 987 | 3 | 0 | 3 | 0 | 14 | |
| RFA_00707 | 0.00 | 0.00 | 0.00 | 0 | 1035 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00715 | 0.00 | 0.00 | 0.00 | 0 | 946 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00717 | 0.00 | 0.00 | 0.00 | 0 | 903 | 0 | 0 | 0 | 0 | 14 | |
| RFA_00730 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00731 | 0.64 | 0.42 | 1.00 | 5 | 898 | 1 | 0 | 0 | 1 | 7 | |
| RFA_00733 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00734 | 0.64 | 0.42 | 1.00 | 5 | 898 | 0 | 0 | 0 | 0 | 7 | |
| RFA_00736 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00737 | 0.64 | 0.42 | 1.00 | 5 | 898 | 1 | 0 | 0 | 1 | 7 | |
| RFA_00745 | 0.50 | 0.25 | 1.00 | 3 | 943 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00749 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00758 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00762 | 0.64 | 0.42 | 1.00 | 5 | 898 | 0 | 0 | 0 | 0 | 7 | |
| RFA_00763 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00764 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00765 | 0.50 | 0.25 | 1.00 | 3 | 900 | 0 | 0 | 0 | 0 | 9 | |
| RFA_00786 | 0.79 | 0.63 | 1.00 | 20 | 5030 | 0 | 0 | 0 | 0 | 12 | |
| RFA_00791 | 0.71 | 0.56 | 0.90 | 18 | 5131 | 2 | 0 | 2 | 0 | 14 | |
| RFA_00792 | 0.81 | 0.72 | 0.92 | 23 | 5025 | 2 | 0 | 2 | 0 | 9 | |
| RFA_00801 | 0.74 | 0.63 | 0.87 | 20 | 5027 | 4 | 0 | 3 | 1 | 12 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.