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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Sfold McQFold
MCC 0.382 > 0.274
Average MCC ± 95% Confidence Intervals 0.455 ± 0.254 > 0.354 ± 0.270
Sensitivity 0.336 > 0.252
Positive Predictive Value 0.435 > 0.300
Total TP 391 > 293
Total TN 2495368 > 2495289
Total FP 828 < 1029
Total FP CONTRA 66 < 130
Total FP INCONS 441 < 554
Total FP COMP 321 < 345
Total FN 774 < 872
P-value 0.0

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Performance plots


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

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

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP 391
Total TN 2495368
Total FP 828
Total FP CONTRA 66
Total FP INCONS 441
Total FP COMP 321
Total FN 774
Total Scores
MCC 0.382
Average MCC ± 95% Confidence Intervals 0.455 ± 0.254
Sensitivity 0.336
Positive Predictive Value 0.435
Nr of predictions 6

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.38 0.31 0.48 80 456322 102 10 78 14 180
CRW_00702 - 0.62 0.60 0.63 45 357364 124 6 20 98 30
CRW_00704 - 0.87 0.86 0.88 81 386668 181 4 7 170 13
CRW_00780 - 0.34 0.29 0.39 75 475607 124 19 99 6 180
CRW_00794 - 0.24 0.22 0.25 55 434562 180 12 149 19 191
CRW_00796 - 0.29 0.23 0.35 55 384845 117 15 88 14 180

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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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