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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric PknotsRG McQFold
MCC 0.383 > 0.301
Average MCC ± 95% Confidence Intervals 0.449 ± 0.199 > 0.371 ± 0.221
Sensitivity 0.378 > 0.283
Positive Predictive Value 0.388 > 0.322
Total TP 501 > 375
Total TN 2834052 < 2834177
Total FP 1291 > 1190
Total FP CONTRA 140 < 152
Total FP INCONS 649 > 638
Total FP COMP 502 > 400
Total FN 825 < 951
P-value 0.0

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Performance plots


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

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

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Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP 501
Total TN 2834052
Total FP 1291
Total FP CONTRA 140
Total FP INCONS 649
Total FP COMP 502
Total FN 825
Total Scores
MCC 0.383
Average MCC ± 95% Confidence Intervals 0.449 ± 0.199
Sensitivity 0.378
Positive Predictive Value 0.388
Nr of predictions 7

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.40 0.37 0.43 96 456268 147 23 103 21 164
CRW_00702 - 0.66 0.72 0.61 54 357346 213 10 25 178 21
CRW_00704 - 0.81 0.80 0.82 75 386669 195 4 12 179 19
CRW_00730 - 0.46 0.51 0.42 82 338879 185 33 82 70 79
CRW_00780 - 0.32 0.31 0.34 79 475565 169 23 133 13 176
CRW_00794 - 0.24 0.24 0.24 58 434539 200 18 163 19 188
CRW_00796 - 0.25 0.24 0.26 57 384786 182 29 131 22 178

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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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