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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 0.371 > 0.274
Average MCC ± 95% Confidence Intervals 0.447 ± 0.247 > 0.354 ± 0.270
Sensitivity 0.360 > 0.252
Positive Predictive Value 0.383 > 0.300
Total TP 419 > 293
Total TN 2495173 < 2495289
Total FP 1106 > 1029
Total FP CONTRA 107 < 130
Total FP INCONS 567 > 554
Total FP COMP 432 > 345
Total FN 746 < 872
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 419
Total TN 2495173
Total FP 1106
Total FP CONTRA 107
Total FP INCONS 567
Total FP COMP 432
Total FN 746
Total Scores
MCC 0.371
Average MCC ± 95% Confidence Intervals 0.447 ± 0.247
Sensitivity 0.360
Positive Predictive Value 0.383
Nr of predictions 6

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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_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 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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