CompaRNA - on-line benchmarks of RNA structure prediction methods
Home

Methods
Datasets
Rankings
RNA 2D Atlas

Help
FAQ

Contact us
RSS feeds
Twitter

Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of RNAfold - scored higher in this pairwise comparison

  4. Performance of McQFold - scored lower in this pairwise comparison

  5. Compile and download dataset for RNAfold & McQFold [.zip] - may take several seconds...


Overview

Metric RNAfold McQFold
MCC 0.350 > 0.301
Average MCC ± 95% Confidence Intervals 0.424 ± 0.221 > 0.371 ± 0.221
Sensitivity 0.348 > 0.283
Positive Predictive Value 0.351 > 0.322
Total TP 462 > 375
Total TN 2834027 < 2834177
Total FP 1333 > 1190
Total FP CONTRA 142 < 152
Total FP INCONS 711 > 638
Total FP COMP 480 > 400
Total FN 864 < 951
P-value 0.0

^top



Performance plots


  1. Comparison of performance of RNAfold and McQFold. 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 RNAfold and McQFold).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for RNAfold and McQFold. 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 RNAfold and McQFold).

^top




Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP 462
Total TN 2834027
Total FP 1333
Total FP CONTRA 142
Total FP INCONS 711
Total FP COMP 480
Total FN 864
Total Scores
MCC 0.350
Average MCC ± 95% Confidence Intervals 0.424 ± 0.221
Sensitivity 0.348
Positive Predictive Value 0.351
Nr of predictions 7

^top


2. Individual counts for RNAfold [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.39 0.36 0.42 93 456267 151 22 108 21 167
CRW_00702 - 0.66 0.72 0.61 54 357347 206 10 24 172 21
CRW_00704 - 0.81 0.80 0.82 75 386669 196 4 12 180 19
CRW_00730 - 0.46 0.53 0.40 86 338863 190 41 86 63 75
CRW_00780 - 0.20 0.19 0.21 49 475564 199 20 167 12 206
CRW_00794 - 0.24 0.24 0.24 58 434537 202 18 165 19 188
CRW_00796 - 0.20 0.20 0.21 47 384780 189 27 149 13 188

^top


Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP 375
Total TN 2834177
Total FP 1190
Total FP CONTRA 152
Total FP INCONS 638
Total FP COMP 400
Total FN 951
Total Scores
MCC 0.301
Average MCC ± 95% Confidence Intervals 0.371 ± 0.221
Sensitivity 0.283
Positive Predictive Value 0.322
Nr of predictions 7

^top


2. Individual counts for McQFold [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.15 0.13 0.18 34 456305 172 19 132 21 226
CRW_00702 - 0.68 0.75 0.62 56 357344 176 25 10 141 19
CRW_00704 - 0.67 0.66 0.68 62 386669 180 11 18 151 32
CRW_00730 - 0.47 0.51 0.44 82 338888 161 22 84 55 79
CRW_00780 - 0.23 0.21 0.25 54 475586 170 24 136 10 201
CRW_00794 - 0.30 0.27 0.32 67 434571 161 24 116 21 179
CRW_00796 - 0.09 0.09 0.11 20 384814 170 27 142 1 215

^top

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.

Copyright© - Adam Mickiewicz University & IIMCB - All rights reserved