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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric ProbKnot McQFold
MCC 0.360 > 0.274
Average MCC ± 95% Confidence Intervals 0.442 ± 0.267 > 0.354 ± 0.270
Sensitivity 0.348 > 0.252
Positive Predictive Value 0.374 > 0.300
Total TP 405 > 293
Total TN 2495182 < 2495289
Total FP 1120 > 1029
Total FP CONTRA 113 < 130
Total FP INCONS 566 > 554
Total FP COMP 441 > 345
Total FN 760 < 872
P-value 0.0

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Performance plots


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

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP 405
Total TN 2495182
Total FP 1120
Total FP CONTRA 113
Total FP INCONS 566
Total FP COMP 441
Total FN 760
Total Scores
MCC 0.360
Average MCC ± 95% Confidence Intervals 0.442 ± 0.267
Sensitivity 0.348
Positive Predictive Value 0.374
Nr of predictions 6

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.29 0.27 0.30 71 456253 185 27 139 19 189
CRW_00702 - 0.68 0.81 0.58 61 357329 217 33 12 172 14
CRW_00704 - 0.84 0.85 0.83 80 386664 204 7 9 188 14
CRW_00780 - 0.26 0.23 0.30 58 475606 150 17 119 14 197
CRW_00794 - 0.28 0.28 0.28 68 434537 200 16 157 27 178
CRW_00796 - 0.30 0.29 0.32 67 384793 164 13 130 21 168

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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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