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 0.332 > 0.274
Average MCC ± 95% Confidence Intervals 0.417 ± 0.274 > 0.354 ± 0.270
Sensitivity 0.323 > 0.252
Positive Predictive Value 0.341 > 0.300
Total TP 376 > 293
Total TN 2495164 < 2495289
Total FP 1143 > 1029
Total FP CONTRA 101 < 130
Total FP INCONS 625 > 554
Total FP COMP 417 > 345
Total FN 789 < 872
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 376
Total TN 2495164
Total FP 1143
Total FP CONTRA 101
Total FP INCONS 625
Total FP COMP 417
Total FN 789
Total Scores
MCC 0.332
Average MCC ± 95% Confidence Intervals 0.417 ± 0.274
Sensitivity 0.323
Positive Predictive Value 0.341
Nr of predictions 6

^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_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 293
Total TN 2495289
Total FP 1029
Total FP CONTRA 130
Total FP INCONS 554
Total FP COMP 345
Total FN 872
Total Scores
MCC 0.274
Average MCC ± 95% Confidence Intervals 0.354 ± 0.270
Sensitivity 0.252
Positive Predictive Value 0.300
Nr of predictions 6

^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_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