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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Afold McQFold
MCC 0.304 > 0.241
Average MCC ± 95% Confidence Intervals 0.366 ± 0.324 > 0.289 ± 0.281
Sensitivity 0.293 > 0.217
Positive Predictive Value 0.317 > 0.267
Total TP 319 > 237
Total TN 2137824 < 2137945
Total FP 941 > 853
Total FP CONTRA 85 < 105
Total FP INCONS 603 > 544
Total FP COMP 253 > 204
Total FN 771 < 853
P-value 0.0

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Performance plots


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

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

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Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 319
Total TN 2137824
Total FP 941
Total FP CONTRA 85
Total FP INCONS 603
Total FP COMP 253
Total FN 771
Total Scores
MCC 0.304
Average MCC ± 95% Confidence Intervals 0.366 ± 0.324
Sensitivity 0.293
Positive Predictive Value 0.317
Nr of predictions 5

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.39 0.36 0.42 93 456266 153 18 113 22 167
CRW_00704 - 0.81 0.80 0.82 75 386669 198 4 12 182 19
CRW_00780 - 0.18 0.18 0.19 45 475569 201 21 165 15 210
CRW_00794 - 0.24 0.24 0.25 59 434543 196 15 161 20 187
CRW_00796 - 0.20 0.20 0.21 47 384777 193 27 152 14 188

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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 237
Total TN 2137945
Total FP 853
Total FP CONTRA 105
Total FP INCONS 544
Total FP COMP 204
Total FN 853
Total Scores
MCC 0.241
Average MCC ± 95% Confidence Intervals 0.289 ± 0.281
Sensitivity 0.217
Positive Predictive Value 0.267
Nr of predictions 5

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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_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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