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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric MaxExpect McQFold
MCC 0.367 > 0.274
Average MCC ± 95% Confidence Intervals 0.451 ± 0.275 > 0.354 ± 0.270
Sensitivity 0.340 > 0.252
Positive Predictive Value 0.397 > 0.300
Total TP 396 > 293
Total TN 2495269 < 2495289
Total FP 987 < 1029
Total FP CONTRA 83 < 130
Total FP INCONS 518 < 554
Total FP COMP 386 > 345
Total FN 769 < 872
P-value 0.0

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Performance plots


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

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

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Performance of MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP 396
Total TN 2495269
Total FP 987
Total FP CONTRA 83
Total FP INCONS 518
Total FP COMP 386
Total FN 769
Total Scores
MCC 0.367
Average MCC ± 95% Confidence Intervals 0.451 ± 0.275
Sensitivity 0.340
Positive Predictive Value 0.397
Nr of predictions 6

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.29 0.25 0.34 65 456299 140 18 108 14 195
CRW_00702 - 0.70 0.76 0.64 57 357346 172 24 8 140 18
CRW_00704 - 0.87 0.86 0.87 81 386667 187 2 10 175 13
CRW_00780 - 0.27 0.24 0.30 61 475598 155 14 127 14 194
CRW_00794 - 0.29 0.28 0.31 68 434558 174 10 142 22 178
CRW_00796 - 0.29 0.27 0.32 64 384801 159 15 123 21 171

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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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