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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric UNAFold McQFold
MCC 0.384 > 0.301
Average MCC ± 95% Confidence Intervals 0.443 ± 0.188 > 0.371 ± 0.221
Sensitivity 0.379 > 0.283
Positive Predictive Value 0.389 > 0.322
Total TP 503 > 375
Total TN 2834050 < 2834177
Total FP 1265 > 1190
Total FP CONTRA 135 < 152
Total FP INCONS 654 > 638
Total FP COMP 476 > 400
Total FN 823 < 951
P-value 0.0

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Performance plots


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

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

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Performance of UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP 503
Total TN 2834050
Total FP 1265
Total FP CONTRA 135
Total FP INCONS 654
Total FP COMP 476
Total FN 823
Total Scores
MCC 0.384
Average MCC ± 95% Confidence Intervals 0.443 ± 0.188
Sensitivity 0.379
Positive Predictive Value 0.389
Nr of predictions 7

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.38 0.36 0.41 93 456264 154 19 114 21 167
CRW_00702 - 0.57 0.64 0.51 48 357341 200 16 30 154 27
CRW_00704 - 0.80 0.79 0.82 74 386670 190 4 12 174 20
CRW_00730 - 0.51 0.55 0.48 88 338891 172 28 69 75 73
CRW_00780 - 0.36 0.35 0.37 89 475561 163 24 126 13 166
CRW_00794 - 0.23 0.23 0.23 56 434530 209 20 172 17 190
CRW_00796 - 0.25 0.23 0.26 55 384793 177 24 131 22 180

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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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