Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
- Performance of Pknots
- scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(seed) & Pknots [.zip] - may take several seconds...
Overview
| Metric |
PETfold_pre2.0(seed) |
|
Pknots |
|---|
| MCC |
0.789 |
>
|
0.577 |
| Average MCC ± 95% Confidence Intervals |
0.768
±
0.077
|
>
|
0.610
±
0.183
|
| Sensitivity |
0.726 |
>
|
0.621 |
| Positive Predictive Value |
0.861 |
>
|
0.545 |
| Total TP |
247 |
>
|
211 |
| Total TN |
30025 |
>
|
29925 |
| Total FP |
87 |
<
|
233 |
| Total FP CONTRA |
17 |
<
|
58 |
| Total FP INCONS |
23 |
<
|
118 |
| Total FP COMP |
47 |
<
|
57 |
| Total FN |
93 |
<
|
129 |
| P-value |
2.52609899389e-08 |
Performance plots
-
Comparison of performance of PETfold_pre2.0(seed) and Pknots. 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 Pknots).
-
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 Pknots).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Pknots. 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 Pknots).
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 |
247 |
| Total TN |
30025 |
| Total FP |
87 |
| Total FP CONTRA |
17 |
| Total FP INCONS |
23 |
| Total FP COMP |
47 |
| Total FN |
93 |
| Total Scores |
|---|
| MCC |
0.789 |
| Average MCC ± 95% Confidence Intervals |
0.768
±
0.077
|
| Sensitivity |
0.726 |
| Positive Predictive Value |
0.861 |
| Nr of predictions |
15 |
Performance of Pknots
- scored lower in this pairwise comparison
1. Total counts & total scores for Pknots
| Total Base Pair Counts |
|---|
| Total TP |
211 |
| Total TN |
29925 |
| Total FP |
233 |
| Total FP CONTRA |
58 |
| Total FP INCONS |
118 |
| Total FP COMP |
57 |
| Total FN |
129 |
| Total Scores |
|---|
| MCC |
0.577 |
| Average MCC ± 95% Confidence Intervals |
0.610
±
0.183
|
| Sensitivity |
0.621 |
| Positive Predictive Value |
0.545 |
| Nr of predictions |
15 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
