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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 Cylofold - scored lower in this pairwise comparison

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


Overview

Metric IPknot Cylofold
MCC 0.648 > 0.271
Average MCC ± 95% Confidence Intervals 0.651 ± 0.807 > 0.275 ± 1.303
Sensitivity 0.584 > 0.241
Positive Predictive Value 0.721 > 0.308
Total TP 80 > 33
Total TN 60477 < 60481
Total FP 32 < 78
Total FP CONTRA 7 > 3
Total FP INCONS 24 < 71
Total FP COMP 1 < 4
Total FN 57 < 104
P-value 0.0

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Performance plots


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

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

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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 80
Total TN 60477
Total FP 32
Total FP CONTRA 7
Total FP INCONS 24
Total FP COMP 1
Total FN 57
Total Scores
MCC 0.648
Average MCC ± 95% Confidence Intervals 0.651 ± 0.807
Sensitivity 0.584
Positive Predictive Value 0.721
Nr of predictions 2

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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
ASE_00408 - 0.71 0.61 0.84 43 32334 8 1 7 0 28
ASE_00429 - 0.59 0.56 0.62 37 28143 24 6 17 1 29

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Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP 33
Total TN 60481
Total FP 78
Total FP CONTRA 3
Total FP INCONS 71
Total FP COMP 4
Total FN 104
Total Scores
MCC 0.271
Average MCC ± 95% Confidence Intervals 0.275 ± 1.303
Sensitivity 0.241
Positive Predictive Value 0.308
Nr of predictions 2

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
ASE_00408 - 0.17 0.15 0.20 11 32329 45 3 42 0 60
ASE_00429 - 0.38 0.33 0.43 22 28152 33 0 29 4 44

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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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