Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
- Performance of CentroidHomfold‑LAST
- scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(seed) & CentroidHomfold‑LAST [.zip] - may take several seconds...
Overview
| Metric |
PETfold_pre2.0(seed) |
|
CentroidHomfold‑LAST |
|---|
| MCC |
0.729 |
>
|
0.683 |
| Average MCC ± 95% Confidence Intervals |
0.718
±
0.056
|
>
|
0.676
±
0.084
|
| Sensitivity |
0.649 |
>
|
0.590 |
| Positive Predictive Value |
0.824 |
>
|
0.794 |
| Total TP |
285 |
>
|
259 |
| Total TN |
54590 |
<
|
54610 |
| Total FP |
70 |
<
|
72 |
| Total FP CONTRA |
33 |
>
|
16 |
| Total FP INCONS |
28 |
<
|
51 |
| Total FP COMP |
9 |
>
|
5 |
| Total FN |
154 |
<
|
180 |
| P-value |
2.89169006118e-08 |
Performance plots
-
Comparison of performance of PETfold_pre2.0(seed) and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).
-
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 CentroidHomfold‑LAST).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and CentroidHomfold-LAST. 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 CentroidHomfold‑LAST).
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 CentroidHomfold‑LAST
- scored lower in this pairwise comparison
1. Total counts & total scores for CentroidHomfold‑LAST
| Total Base Pair Counts |
|---|
| Total TP |
259 |
| Total TN |
54610 |
| Total FP |
72 |
| Total FP CONTRA |
16 |
| Total FP INCONS |
51 |
| Total FP COMP |
5 |
| Total FN |
180 |
| Total Scores |
|---|
| MCC |
0.683 |
| Average MCC ± 95% Confidence Intervals |
0.676
±
0.084
|
| Sensitivity |
0.590 |
| Positive Predictive Value |
0.794 |
| Nr of predictions |
19 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
