Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
- Performance of HotKnots
- scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(seed) & HotKnots [.zip] - may take several seconds...
Overview
| Metric |
PETfold_pre2.0(seed) |
|
HotKnots |
|---|
| MCC |
0.722 |
>
|
0.504 |
| Average MCC ± 95% Confidence Intervals |
0.699
±
0.062
|
>
|
0.513
±
0.106
|
| Sensitivity |
0.595 |
>
|
0.450 |
| Positive Predictive Value |
0.879 |
>
|
0.570 |
| Total TP |
547 |
>
|
414 |
| Total TN |
135398 |
>
|
135294 |
| Total FP |
106 |
<
|
355 |
| Total FP CONTRA |
8 |
<
|
33 |
| Total FP INCONS |
67 |
<
|
279 |
| Total FP COMP |
31 |
<
|
43 |
| Total FN |
372 |
<
|
505 |
| P-value |
3.56938820447e-08 |
Performance plots
-
Comparison of performance of PETfold_pre2.0(seed) and HotKnots. 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(seed)
and HotKnots).
-
Comparison of performance of PETfold_pre2.0(seed) and HotKnots. 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(seed)
and HotKnots).
-
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(seed)
and HotKnots).
-
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(seed)
and HotKnots).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and HotKnots. 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(seed)
and HotKnots).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and HotKnots. 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(seed)
and HotKnots).
Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
1. Total counts & total scores for PETfold_pre2.0(seed)
| Total Base Pair Counts |
|---|
| Total TP |
547 |
| Total TN |
135398 |
| Total FP |
106 |
| Total FP CONTRA |
8 |
| Total FP INCONS |
67 |
| Total FP COMP |
31 |
| Total FN |
372 |
| Total Scores |
|---|
| MCC |
0.722 |
| Average MCC ± 95% Confidence Intervals |
0.699
±
0.062
|
| Sensitivity |
0.595 |
| Positive Predictive Value |
0.879 |
| Nr of predictions |
25 |
Performance of HotKnots
- scored lower in this pairwise comparison
1. Total counts & total scores for HotKnots
| Total Base Pair Counts |
|---|
| Total TP |
414 |
| Total TN |
135294 |
| Total FP |
355 |
| Total FP CONTRA |
33 |
| Total FP INCONS |
279 |
| Total FP COMP |
43 |
| Total FN |
505 |
| Total Scores |
|---|
| MCC |
0.504 |
| Average MCC ± 95% Confidence Intervals |
0.513
±
0.106
|
| Sensitivity |
0.450 |
| Positive Predictive Value |
0.570 |
| Nr of predictions |
25 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
