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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 0.365 > 0.274
Average MCC ± 95% Confidence Intervals 0.432 ± 0.231 > 0.354 ± 0.270
Sensitivity 0.356 > 0.252
Positive Predictive Value 0.375 > 0.300
Total TP 415 > 293
Total TN 2495159 < 2495289
Total FP 1093 > 1029
Total FP CONTRA 107 < 130
Total FP INCONS 585 > 554
Total FP COMP 401 > 345
Total FN 750 < 872
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 415
Total TN 2495159
Total FP 1093
Total FP CONTRA 107
Total FP INCONS 585
Total FP COMP 401
Total FN 750
Total Scores
MCC 0.365
Average MCC ± 95% Confidence Intervals 0.432 ± 0.231
Sensitivity 0.356
Positive Predictive Value 0.375
Nr of predictions 6

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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_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 293
Total TN 2495289
Total FP 1029
Total FP CONTRA 130
Total FP INCONS 554
Total FP COMP 345
Total FN 872
Total Scores
MCC 0.274
Average MCC ± 95% Confidence Intervals 0.354 ± 0.270
Sensitivity 0.252
Positive Predictive Value 0.300
Nr of predictions 6

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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_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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