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 Contrafold - scored higher in this pairwise comparison

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

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


Overview

Metric Contrafold McQFold
MCC 0.428 > 0.301
Average MCC ± 95% Confidence Intervals 0.494 ± 0.201 > 0.371 ± 0.221
Sensitivity 0.386 > 0.283
Positive Predictive Value 0.476 > 0.322
Total TP 512 > 375
Total TN 2834266 > 2834177
Total FP 1060 < 1190
Total FP CONTRA 74 < 152
Total FP INCONS 490 < 638
Total FP COMP 496 > 400
Total FN 814 < 951
P-value 0.0

^top



Performance plots


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

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

^top




Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP 512
Total TN 2834266
Total FP 1060
Total FP CONTRA 74
Total FP INCONS 490
Total FP COMP 496
Total FN 814
Total Scores
MCC 0.428
Average MCC ± 95% Confidence Intervals 0.494 ± 0.201
Sensitivity 0.386
Positive Predictive Value 0.476
Nr of predictions 7

^top


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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.34 0.26 0.43 68 456333 107 8 81 18 192
CRW_00702 - 0.72 0.73 0.71 55 357357 187 7 16 164 20
CRW_00704 - 0.87 0.87 0.87 82 386666 195 4 8 183 12
CRW_00730 - 0.48 0.49 0.48 79 338910 157 15 72 70 82
CRW_00780 - 0.32 0.29 0.35 74 475591 151 18 117 16 181
CRW_00794 - 0.37 0.35 0.39 85 434558 154 20 115 19 161
CRW_00796 - 0.36 0.29 0.45 69 384851 109 2 81 26 166

^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