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

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric RNAfold Cylofold
MCC 0.446 > 0.271
Average MCC ± 95% Confidence Intervals 0.444 ± 0.654 > 0.275 ± 1.303
Sensitivity 0.431 > 0.241
Positive Predictive Value 0.465 > 0.308
Total TP 59 > 33
Total TN 60461 < 60481
Total FP 80 > 78
Total FP CONTRA 3 = 3
Total FP INCONS 65 < 71
Total FP COMP 12 > 4
Total FN 78 < 104
P-value 0.0

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Performance plots


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

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

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Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP 59
Total TN 60461
Total FP 80
Total FP CONTRA 3
Total FP INCONS 65
Total FP COMP 12
Total FN 78
Total Scores
MCC 0.446
Average MCC ± 95% Confidence Intervals 0.444 ± 0.654
Sensitivity 0.431
Positive Predictive Value 0.465
Nr of predictions 2

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
ASE_00408 - 0.50 0.48 0.52 34 32319 36 2 30 4 37
ASE_00429 - 0.39 0.38 0.41 25 28142 44 1 35 8 41

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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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