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 Carnac(seed) - scored lower in this pairwise comparison

  5. Compile and download dataset for Sfold & Carnac(seed) [.zip] - may take several seconds...


Overview

Metric Sfold Carnac(seed)
MCC 0.798 > 0.729
Average MCC ± 95% Confidence Intervals 0.798 ± > 0.729 ±
Sensitivity 0.769 > 0.570
Positive Predictive Value 0.828 < 0.932
Total TP 352 > 261
Total TN 1085176 < 1085321
Total FP 112 > 35
Total FP CONTRA 13 > 6
Total FP INCONS 60 > 13
Total FP COMP 39 > 16
Total FN 106 < 197
P-value 0.0

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Performance plots


  1. Comparison of performance of Sfold and Carnac(seed). 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 Carnac(seed)).

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

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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 352
Total TN 1085176
Total FP 112
Total FP CONTRA 13
Total FP INCONS 60
Total FP COMP 39
Total FN 106
Total Scores
MCC 0.798
Average MCC ± 95% Confidence Intervals 0.798 ±
Sensitivity 0.769
Positive Predictive Value 0.828
Nr of predictions 1

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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
CRW_00024

SSU_rRNA_archaea links to Rfam database...

0.80 0.77 0.83 352 1085176 112 13 60 39 106

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Performance of Carnac(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for Carnac(seed)

Total Base Pair Counts
Total TP 261
Total TN 1085321
Total FP 35
Total FP CONTRA 6
Total FP INCONS 13
Total FP COMP 16
Total FN 197
Total Scores
MCC 0.729
Average MCC ± 95% Confidence Intervals 0.729 ±
Sensitivity 0.570
Positive Predictive Value 0.932
Nr of predictions 1

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2. Individual counts for Carnac(seed) [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024

SSU_rRNA_archaea links to Rfam database...

0.73 0.57 0.93 261 1085321 35 6 13 16 197

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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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