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 MaxExpect - scored lower in this pairwise comparison

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


Overview

Metric Carnac(seed) MaxExpect
MCC 0.729 > 0.706
Average MCC ± 95% Confidence Intervals 0.729 ± > 0.706 ±
Sensitivity 0.570 < 0.699
Positive Predictive Value 0.932 > 0.713
Total TP 261 < 320
Total TN 1085321 > 1085152
Total FP 35 < 169
Total FP CONTRA 6 < 17
Total FP INCONS 13 < 112
Total FP COMP 16 < 40
Total FN 197 > 138
P-value 0.0

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Performance plots


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

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

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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 MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP 320
Total TN 1085152
Total FP 169
Total FP CONTRA 17
Total FP INCONS 112
Total FP COMP 40
Total FN 138
Total Scores
MCC 0.706
Average MCC ± 95% Confidence Intervals 0.706 ±
Sensitivity 0.699
Positive Predictive Value 0.713
Nr of predictions 1

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2. Individual counts for MaxExpect [ 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...

0.71 0.70 0.71 320 1085152 169 17 112 40 138

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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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