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 IPknot - scored higher in this pairwise comparison

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

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


Overview

Metric IPknot McQFold
MCC 0.426 > 0.301
Average MCC ± 95% Confidence Intervals 0.499 ± 0.250 > 0.371 ± 0.221
Sensitivity 0.337 > 0.283
Positive Predictive Value 0.539 > 0.322
Total TP 447 > 375
Total TN 2834512 > 2834177
Total FP 748 < 1190
Total FP CONTRA 74 < 152
Total FP INCONS 309 < 638
Total FP COMP 365 < 400
Total FN 879 < 951
P-value 0.0

^top



Performance plots


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

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

^top




Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP 447
Total TN 2834512
Total FP 748
Total FP CONTRA 74
Total FP INCONS 309
Total FP COMP 365
Total FN 879
Total Scores
MCC 0.426
Average MCC ± 95% Confidence Intervals 0.499 ± 0.250
Sensitivity 0.337
Positive Predictive Value 0.539
Nr of predictions 7

^top


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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.33 0.23 0.46 61 456358 81 9 62 10 199
CRW_00702 - 0.86 0.83 0.89 62 357365 141 7 1 133 13
CRW_00704 - 0.91 0.90 0.92 85 386668 146 4 3 139 9
CRW_00730 - 0.46 0.45 0.46 73 338918 141 20 65 56 88
CRW_00780 - 0.29 0.21 0.39 54 475662 88 18 66 4 201
CRW_00794 - 0.37 0.28 0.49 68 434640 81 10 60 11 178
CRW_00796 - 0.28 0.19 0.43 44 384901 70 6 52 12 191

^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