CompaRNA - on-line benchmarks of RNA structure prediction methods
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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 0.420 > 0.274
Average MCC ± 95% Confidence Intervals 0.496 ± 0.249 > 0.354 ± 0.270
Sensitivity 0.372 > 0.252
Positive Predictive Value 0.476 > 0.300
Total TP 433 > 293
Total TN 2495356 > 2495289
Total FP 903 < 1029
Total FP CONTRA 59 < 130
Total FP INCONS 418 < 554
Total FP COMP 426 > 345
Total FN 732 < 872
P-value 0.0

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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).

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP 433
Total TN 2495356
Total FP 903
Total FP CONTRA 59
Total FP INCONS 418
Total FP COMP 426
Total FN 732
Total Scores
MCC 0.420
Average MCC ± 95% Confidence Intervals 0.496 ± 0.249
Sensitivity 0.372
Positive Predictive Value 0.476
Nr of predictions 6

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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_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

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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

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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

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

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