CompaRNA - on-line benchmarks of RNA structure prediction methods
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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Fold Cylofold
MCC 0.597 > 0.271
Average MCC ± 95% Confidence Intervals 0.593 ± 0.688 > 0.275 ± 1.303
Sensitivity 0.591 > 0.241
Positive Predictive Value 0.604 > 0.308
Total TP 81 > 33
Total TN 60454 < 60481
Total FP 67 < 78
Total FP CONTRA 6 > 3
Total FP INCONS 47 < 71
Total FP COMP 14 > 4
Total FN 56 < 104
P-value 0.0

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Performance plots


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

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP 81
Total TN 60454
Total FP 67
Total FP CONTRA 6
Total FP INCONS 47
Total FP COMP 14
Total FN 56
Total Scores
MCC 0.597
Average MCC ± 95% Confidence Intervals 0.593 ± 0.688
Sensitivity 0.591
Positive Predictive Value 0.604
Nr of predictions 2

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
ASE_00408 - 0.65 0.66 0.64 47 32311 32 4 23 5 24
ASE_00429 - 0.54 0.52 0.57 34 28143 35 2 24 9 32

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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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