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 |
0.715 |
>
|
0.587 |
| Average MCC ± 95% Confidence Intervals |
0.699
±
0.059
|
>
|
0.568
±
0.095
|
| Sensitivity |
0.602 |
>
|
0.490 |
| Positive Predictive Value |
0.850 |
>
|
0.703 |
| Total TP |
935 |
>
|
761 |
| Total TN |
1251685 |
<
|
1251702 |
| Total FP |
203 |
<
|
361 |
| Total FP CONTRA |
18 |
<
|
28 |
| Total FP INCONS |
147 |
<
|
294 |
| Total FP COMP |
38 |
<
|
39 |
| Total FN |
617 |
<
|
791 |
| P-value |
5.23657817852e-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).
-
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).
-
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).
-
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 |
935 |
| Total TN |
1251685 |
| Total FP |
203 |
| Total FP CONTRA |
18 |
| Total FP INCONS |
147 |
| Total FP COMP |
38 |
| Total FN |
617 |
| Total Scores |
|---|
| MCC |
0.715 |
| Average MCC ± 95% Confidence Intervals |
0.699
±
0.059
|
| Sensitivity |
0.602 |
| Positive Predictive Value |
0.850 |
| Nr of predictions |
26 |
Performance of IPknot
- scored lower in this pairwise comparison
1. Total counts & total scores for IPknot
| Total Base Pair Counts |
|---|
| Total TP |
761 |
| Total TN |
1251702 |
| Total FP |
361 |
| Total FP CONTRA |
28 |
| Total FP INCONS |
294 |
| Total FP COMP |
39 |
| Total FN |
791 |
| Total Scores |
|---|
| MCC |
0.587 |
| Average MCC ± 95% Confidence Intervals |
0.568
±
0.095
|
| Sensitivity |
0.490 |
| Positive Predictive Value |
0.703 |
| Nr of predictions |
26 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
