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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric IPknot McQFold
MCC 0.422 > 0.274
Average MCC ± 95% Confidence Intervals 0.506 ± 0.310 > 0.354 ± 0.270
Sensitivity 0.321 > 0.252
Positive Predictive Value 0.557 > 0.300
Total TP 374 > 293
Total TN 2495594 > 2495289
Total FP 607 < 1029
Total FP CONTRA 54 < 130
Total FP INCONS 244 < 554
Total FP COMP 309 < 345
Total FN 791 < 872
P-value 0.0

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Performance plots


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

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

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP 374
Total TN 2495594
Total FP 607
Total FP CONTRA 54
Total FP INCONS 244
Total FP COMP 309
Total FN 791
Total Scores
MCC 0.422
Average MCC ± 95% Confidence Intervals 0.506 ± 0.310
Sensitivity 0.321
Positive Predictive Value 0.557
Nr of predictions 6

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00443 - 0.33 0.23 0.46 61 456358 81 9 62 10 199
CRW_00702 - 0.86 0.83 0.89 62 357365 141 7 1 133 13
CRW_00704 - 0.91 0.90 0.92 85 386668 146 4 3 139 9
CRW_00780 - 0.29 0.21 0.39 54 475662 88 18 66 4 201
CRW_00794 - 0.37 0.28 0.49 68 434640 81 10 60 11 178
CRW_00796 - 0.28 0.19 0.43 44 384901 70 6 52 12 191

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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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