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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric CentroidFold McQFold
MCC 0.427 > 0.274
Average MCC ± 95% Confidence Intervals 0.504 ± 0.267 > 0.354 ± 0.270
Sensitivity 0.335 > 0.252
Positive Predictive Value 0.545 > 0.300
Total TP 390 > 293
Total TN 2495551 > 2495289
Total FP 675 < 1029
Total FP CONTRA 43 < 130
Total FP INCONS 282 < 554
Total FP COMP 350 > 345
Total FN 775 < 872
P-value 0.0

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Performance plots


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

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

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Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP 390
Total TN 2495551
Total FP 675
Total FP CONTRA 43
Total FP INCONS 282
Total FP COMP 350
Total FN 775
Total Scores
MCC 0.427
Average MCC ± 95% Confidence Intervals 0.504 ± 0.267
Sensitivity 0.335
Positive Predictive Value 0.545
Nr of predictions 6

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.31 0.21 0.45 55 456367 78 4 64 10 205
CRW_00702 - 0.76 0.73 0.80 55 357366 141 5 9 127 20
CRW_00704 - 0.89 0.87 0.91 82 386670 176 3 5 168 12
CRW_00780 - 0.34 0.28 0.42 71 475629 114 18 82 14 184
CRW_00794 - 0.36 0.29 0.44 72 434613 106 13 80 13 174
CRW_00796 - 0.36 0.23 0.57 55 384906 60 0 42 18 180

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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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