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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Fold McQFold
MCC 0.386 > 0.301
Average MCC ± 95% Confidence Intervals 0.457 ± 0.217 > 0.371 ± 0.221
Sensitivity 0.386 > 0.283
Positive Predictive Value 0.386 > 0.322
Total TP 512 > 375
Total TN 2834016 < 2834177
Total FP 1297 > 1190
Total FP CONTRA 148 < 152
Total FP INCONS 666 > 638
Total FP COMP 483 > 400
Total FN 814 < 951
P-value 0.0

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Performance plots


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

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP 512
Total TN 2834016
Total FP 1297
Total FP CONTRA 148
Total FP INCONS 666
Total FP COMP 483
Total FN 814
Total Scores
MCC 0.386
Average MCC ± 95% Confidence Intervals 0.457 ± 0.217
Sensitivity 0.386
Positive Predictive Value 0.386
Nr of predictions 7

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.24 0.23 0.25 59 456251 195 29 151 15 201
CRW_00702 - 0.62 0.77 0.50 58 357319 208 43 15 150 17
CRW_00704 - 0.87 0.87 0.86 82 386665 190 4 9 177 12
CRW_00730 - 0.54 0.58 0.51 94 338891 170 23 68 79 67
CRW_00780 - 0.25 0.24 0.26 60 475567 188 23 150 15 195
CRW_00794 - 0.28 0.28 0.28 70 434531 199 17 160 22 176
CRW_00796 - 0.40 0.38 0.42 89 384792 147 9 113 25 146

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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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