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 ProbKnot - scored higher in this pairwise comparison

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

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


Overview

Metric ProbKnot McQFold
MCC 0.385 > 0.301
Average MCC ± 95% Confidence Intervals 0.458 ± 0.218 > 0.371 ± 0.221
Sensitivity 0.376 > 0.283
Positive Predictive Value 0.395 > 0.322
Total TP 499 > 375
Total TN 2834079 < 2834177
Total FP 1281 > 1190
Total FP CONTRA 132 < 152
Total FP INCONS 632 < 638
Total FP COMP 517 > 400
Total FN 827 < 951
P-value 0.0

^top



Performance plots


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

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

^top




Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP 499
Total TN 2834079
Total FP 1281
Total FP CONTRA 132
Total FP INCONS 632
Total FP COMP 517
Total FN 827
Total Scores
MCC 0.385
Average MCC ± 95% Confidence Intervals 0.458 ± 0.218
Sensitivity 0.376
Positive Predictive Value 0.395
Nr of predictions 7

^top


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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.29 0.27 0.30 71 456253 185 27 139 19 189
CRW_00702 - 0.68 0.81 0.58 61 357329 217 33 12 172 14
CRW_00704 - 0.84 0.85 0.83 80 386664 204 7 9 188 14
CRW_00730 - 0.55 0.58 0.53 94 338897 161 19 66 76 67
CRW_00780 - 0.26 0.23 0.30 58 475606 150 17 119 14 197
CRW_00794 - 0.28 0.28 0.28 68 434537 200 16 157 27 178
CRW_00796 - 0.30 0.29 0.32 67 384793 164 13 130 21 168

^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