Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(20)
- scored higher in this pairwise comparison
- Performance of Contrafold
- scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(20) & Contrafold [.zip] - may take several seconds...
Overview
| Metric |
PETfold_pre2.0(20) |
|
Contrafold |
|---|
| MCC |
0.793 |
>
|
0.627 |
| Average MCC ± 95% Confidence Intervals |
0.752
±
0.129
|
>
|
0.612
±
0.131
|
| Sensitivity |
0.776 |
>
|
0.657 |
| Positive Predictive Value |
0.815 |
>
|
0.607 |
| Total TP |
339 |
>
|
287 |
| Total TN |
41984 |
>
|
41927 |
| Total FP |
145 |
<
|
285 |
| Total FP CONTRA |
14 |
<
|
56 |
| Total FP INCONS |
63 |
<
|
130 |
| Total FP COMP |
68 |
<
|
99 |
| Total FN |
98 |
<
|
150 |
| P-value |
3.18846395401e-08 |
Performance plots
-
Comparison of performance of PETfold_pre2.0(20) 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(20)
and Contrafold).
-
Comparison of performance of PETfold_pre2.0(20) 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(20)
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(20)
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(20)
and Contrafold).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) 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(20)
and Contrafold).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) 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(20)
and Contrafold).
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 |
339 |
| Total TN |
41984 |
| Total FP |
145 |
| Total FP CONTRA |
14 |
| Total FP INCONS |
63 |
| Total FP COMP |
68 |
| Total FN |
98 |
| Total Scores |
|---|
| MCC |
0.793 |
| Average MCC ± 95% Confidence Intervals |
0.752
±
0.129
|
| Sensitivity |
0.776 |
| Positive Predictive Value |
0.815 |
| Nr of predictions |
18 |
Performance of Contrafold
- scored lower in this pairwise comparison
1. Total counts & total scores for Contrafold
| Total Base Pair Counts |
|---|
| Total TP |
287 |
| Total TN |
41927 |
| Total FP |
285 |
| Total FP CONTRA |
56 |
| Total FP INCONS |
130 |
| Total FP COMP |
99 |
| Total FN |
150 |
| Total Scores |
|---|
| MCC |
0.627 |
| Average MCC ± 95% Confidence Intervals |
0.612
±
0.131
|
| Sensitivity |
0.657 |
| Positive Predictive Value |
0.607 |
| Nr of predictions |
18 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
