Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
- Performance of Contrafold
- scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(seed) & Contrafold [.zip] - may take several seconds...
Overview
| Metric |
PETfold_pre2.0(seed) |
|
Contrafold |
|---|
| MCC |
0.866 |
>
|
0.689 |
| Average MCC ± 95% Confidence Intervals |
0.837
±
0.059
|
>
|
0.662
±
0.102
|
| Sensitivity |
0.841 |
>
|
0.703 |
| Positive Predictive Value |
0.892 |
>
|
0.677 |
| Total TP |
858 |
>
|
717 |
| Total TN |
473383 |
>
|
473286 |
| Total FP |
280 |
<
|
513 |
| Total FP CONTRA |
35 |
<
|
91 |
| Total FP INCONS |
69 |
<
|
251 |
| Total FP COMP |
176 |
>
|
171 |
| Total FN |
162 |
<
|
303 |
| P-value |
5.19332990918e-08 |
Performance plots
-
Comparison of performance of PETfold_pre2.0(seed) and Contrafold. 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 Contrafold).
-
Comparison of performance of PETfold_pre2.0(seed) and Contrafold. 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 Contrafold).
-
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 Contrafold).
-
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 Contrafold).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Contrafold. 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 Contrafold).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Contrafold. 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 Contrafold).
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 |
858 |
| Total TN |
473383 |
| Total FP |
280 |
| Total FP CONTRA |
35 |
| Total FP INCONS |
69 |
| Total FP COMP |
176 |
| Total FN |
162 |
| Total Scores |
|---|
| MCC |
0.866 |
| Average MCC ± 95% Confidence Intervals |
0.837
±
0.059
|
| Sensitivity |
0.841 |
| Positive Predictive Value |
0.892 |
| Nr of predictions |
26 |
Performance of Contrafold
- scored lower in this pairwise comparison
1. Total counts & total scores for Contrafold
| Total Base Pair Counts |
|---|
| Total TP |
717 |
| Total TN |
473286 |
| Total FP |
513 |
| Total FP CONTRA |
91 |
| Total FP INCONS |
251 |
| Total FP COMP |
171 |
| Total FN |
303 |
| Total Scores |
|---|
| MCC |
0.689 |
| Average MCC ± 95% Confidence Intervals |
0.662
±
0.102
|
| Sensitivity |
0.703 |
| Positive Predictive Value |
0.677 |
| Nr of predictions |
26 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
