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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of Sfold - scored higher in this pairwise comparison

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

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


Overview

Metric Sfold McQFold
MCC 0.401 > 0.301
Average MCC ± 95% Confidence Intervals 0.464 ± 0.206 > 0.371 ± 0.221
Sensitivity 0.363 > 0.283
Positive Predictive Value 0.443 > 0.322
Total TP 481 > 375
Total TN 2834256 > 2834177
Total FP 986 < 1190
Total FP CONTRA 95 < 152
Total FP INCONS 510 < 638
Total FP COMP 381 < 400
Total FN 845 < 951
P-value 0.0

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Performance plots


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

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

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP 481
Total TN 2834256
Total FP 986
Total FP CONTRA 95
Total FP INCONS 510
Total FP COMP 381
Total FN 845
Total Scores
MCC 0.401
Average MCC ± 95% Confidence Intervals 0.464 ± 0.206
Sensitivity 0.363
Positive Predictive Value 0.443
Nr of predictions 7

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.38 0.31 0.48 80 456322 102 10 78 14 180
CRW_00702 - 0.62 0.60 0.63 45 357364 124 6 20 98 30
CRW_00704 - 0.87 0.86 0.88 81 386668 181 4 7 170 13
CRW_00730 - 0.52 0.56 0.48 90 338888 158 29 69 60 71
CRW_00780 - 0.34 0.29 0.39 75 475607 124 19 99 6 180
CRW_00794 - 0.24 0.22 0.25 55 434562 180 12 149 19 191
CRW_00796 - 0.29 0.23 0.35 55 384845 117 15 88 14 180

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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 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

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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_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

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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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