Table of contents:
- Overview
- Performance Plots
- Performance of CentroidHomfold‑LAST
- scored higher in this pairwise comparison
- Performance of ProbKnot
- scored lower in this pairwise comparison
- Compile and download dataset for CentroidHomfold‑LAST & ProbKnot [.zip] - may take several seconds...
Overview
Metric |
CentroidHomfold‑LAST |
|
ProbKnot |
MCC |
0.708 |
>
|
0.668 |
Average MCC ± 95% Confidence Intervals |
0.752
±
0.089
|
>
|
0.722
±
0.089
|
Sensitivity |
0.629 |
<
|
0.695 |
Positive Predictive Value |
0.803 |
>
|
0.650 |
Total TP |
651 |
<
|
719 |
Total TN |
102789 |
>
|
102493 |
Total FP |
239 |
<
|
527 |
Total FP CONTRA |
43 |
<
|
133 |
Total FP INCONS |
117 |
<
|
255 |
Total FP COMP |
79 |
<
|
139 |
Total FN |
384 |
>
|
316 |
P-value |
3.56938820447e-08 |
Performance plots
-
Comparison of performance of CentroidHomfold-LAST and ProbKnot. 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 CentroidHomfold‑LAST
and ProbKnot).
-
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 CentroidHomfold‑LAST
and ProbKnot).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST and ProbKnot. 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 CentroidHomfold‑LAST
and ProbKnot).
Performance of CentroidHomfold‑LAST
- scored higher in this pairwise comparison
1. Total counts & total scores for CentroidHomfold‑LAST
Total Base Pair Counts |
Total TP |
651 |
Total TN |
102789 |
Total FP |
239 |
Total FP CONTRA |
43 |
Total FP INCONS |
117 |
Total FP COMP |
79 |
Total FN |
384 |
Total Scores |
MCC |
0.708 |
Average MCC ± 95% Confidence Intervals |
0.752
±
0.089
|
Sensitivity |
0.629 |
Positive Predictive Value |
0.803 |
Nr of predictions |
56 |
Performance of ProbKnot
- scored lower in this pairwise comparison
1. Total counts & total scores for ProbKnot
Total Base Pair Counts |
Total TP |
719 |
Total TN |
102493 |
Total FP |
527 |
Total FP CONTRA |
133 |
Total FP INCONS |
255 |
Total FP COMP |
139 |
Total FN |
316 |
Total Scores |
MCC |
0.668 |
Average MCC ± 95% Confidence Intervals |
0.722
±
0.089
|
Sensitivity |
0.695 |
Positive Predictive Value |
0.650 |
Nr of predictions |
56 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
|