Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
- Performance of IPknot
- scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(seed) & IPknot [.zip] - may take several seconds...
Overview
| Metric |
PETfold_pre2.0(seed) |
|
IPknot |
|---|
| MCC |
0.729 |
>
|
0.680 |
| Average MCC ± 95% Confidence Intervals |
0.718
±
0.056
|
>
|
0.680
±
0.106
|
| Sensitivity |
0.649 |
>
|
0.610 |
| Positive Predictive Value |
0.824 |
>
|
0.761 |
| Total TP |
285 |
>
|
268 |
| Total TN |
54590 |
>
|
54584 |
| Total FP |
70 |
<
|
94 |
| Total FP CONTRA |
33 |
>
|
16 |
| Total FP INCONS |
28 |
<
|
68 |
| Total FP COMP |
9 |
<
|
10 |
| Total FN |
154 |
<
|
171 |
| P-value |
3.51155234096e-08 |
Performance plots
-
Comparison of performance of PETfold_pre2.0(seed) and IPknot. 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 IPknot).
-
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 IPknot).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and IPknot. 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 IPknot).
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 |
285 |
| Total TN |
54590 |
| Total FP |
70 |
| Total FP CONTRA |
33 |
| Total FP INCONS |
28 |
| Total FP COMP |
9 |
| Total FN |
154 |
| Total Scores |
|---|
| MCC |
0.729 |
| Average MCC ± 95% Confidence Intervals |
0.718
±
0.056
|
| Sensitivity |
0.649 |
| Positive Predictive Value |
0.824 |
| Nr of predictions |
19 |
Performance of IPknot
- scored lower in this pairwise comparison
1. Total counts & total scores for IPknot
| Total Base Pair Counts |
|---|
| Total TP |
268 |
| Total TN |
54584 |
| Total FP |
94 |
| Total FP CONTRA |
16 |
| Total FP INCONS |
68 |
| Total FP COMP |
10 |
| Total FN |
171 |
| Total Scores |
|---|
| MCC |
0.680 |
| Average MCC ± 95% Confidence Intervals |
0.680
±
0.106
|
| Sensitivity |
0.610 |
| Positive Predictive Value |
0.761 |
| Nr of predictions |
19 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
