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

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Sfold Cylofold
MCC 0.657 > 0.271
Average MCC ± 95% Confidence Intervals 0.658 ± 0.078 > 0.275 ± 1.303
Sensitivity 0.562 > 0.241
Positive Predictive Value 0.770 > 0.308
Total TP 77 > 33
Total TN 60488 > 60481
Total FP 28 < 78
Total FP CONTRA 4 > 3
Total FP INCONS 19 < 71
Total FP COMP 5 > 4
Total FN 60 < 104
P-value 0.0

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Performance plots


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

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

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Performance of Sfold - scored higher in this pairwise comparison

1. Total counts & total scores for Sfold

Total Base Pair Counts
Total TP 77
Total TN 60488
Total FP 28
Total FP CONTRA 4
Total FP INCONS 19
Total FP COMP 5
Total FN 60
Total Scores
MCC 0.657
Average MCC ± 95% Confidence Intervals 0.658 ± 0.078
Sensitivity 0.562
Positive Predictive Value 0.770
Nr of predictions 2

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
ASE_00408 - 0.65 0.56 0.75 40 32332 18 1 12 5 31
ASE_00429 - 0.66 0.56 0.79 37 28156 10 3 7 0 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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