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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric ContextFold McQFold
MCC 0.614 > 0.301
Average MCC ± 95% Confidence Intervals 0.619 ± 0.106 > 0.371 ± 0.221
Sensitivity 0.561 > 0.283
Positive Predictive Value 0.672 > 0.322
Total TP 744 > 375
Total TN 2834235 > 2834177
Total FP 730 < 1190
Total FP CONTRA 78 < 152
Total FP INCONS 285 < 638
Total FP COMP 367 < 400
Total FN 582 < 951
P-value 0.0

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Performance plots


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

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

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP 744
Total TN 2834235
Total FP 730
Total FP CONTRA 78
Total FP INCONS 285
Total FP COMP 367
Total FN 582
Total Scores
MCC 0.614
Average MCC ± 95% Confidence Intervals 0.619 ± 0.106
Sensitivity 0.561
Positive Predictive Value 0.672
Nr of predictions 7

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.61 0.53 0.70 138 456292 71 7 53 11 122
CRW_00702 - 0.74 0.79 0.69 59 357350 156 19 7 130 16
CRW_00704 - 0.58 0.54 0.61 51 386677 165 11 21 133 43
CRW_00730 - 0.56 0.57 0.55 92 338909 135 20 55 60 69
CRW_00780 - 0.81 0.73 0.90 185 475594 40 5 16 19 70
CRW_00794 - 0.57 0.50 0.64 123 434586 76 10 59 7 123
CRW_00796 - 0.47 0.41 0.55 96 384827 87 6 74 7 139

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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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