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

  1. Overview

  2. Performance Plots

  3. Performance of Carnac(seed) - scored higher in this pairwise comparison

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

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


Overview

Metric Carnac(seed) Fold
MCC 0.729 > 0.563
Average MCC ± 95% Confidence Intervals 0.729 ± > 0.563 ±
Sensitivity 0.570 > 0.566
Positive Predictive Value 0.932 > 0.562
Total TP 261 > 259
Total TN 1085321 > 1085140
Total FP 35 < 238
Total FP CONTRA 6 < 22
Total FP INCONS 13 < 180
Total FP COMP 16 < 36
Total FN 197 < 199
P-value 0.0

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Performance plots


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

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

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

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP 259
Total TN 1085140
Total FP 238
Total FP CONTRA 22
Total FP INCONS 180
Total FP COMP 36
Total FN 199
Total Scores
MCC 0.563
Average MCC ± 95% Confidence Intervals 0.563 ±
Sensitivity 0.566
Positive Predictive Value 0.562
Nr of predictions 1

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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
CRW_00024

SSU_rRNA_archaea links to Rfam database...

0.56 0.57 0.56 259 1085140 238 22 180 36 199

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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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