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

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Afold CRWrnafold
MCC 0.477 > 0.343
Average MCC ± 95% Confidence Intervals 0.533 ± 0.420 > 0.376 ± 0.610
Sensitivity 0.520 > 0.373
Positive Predictive Value 0.448 > 0.329
Total TP 39 > 28
Total TN 6705 < 6707
Total FP 66 < 75
Total FP CONTRA 14 = 14
Total FP INCONS 34 < 43
Total FP COMP 18 = 18
Total FN 36 < 47
P-value 0.0

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Performance plots


  1. Comparison of performance of Afold and CRWrnafold. 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 Afold and CRWrnafold).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and CRWrnafold. 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 Afold and CRWrnafold).

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Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 39
Total TN 6705
Total FP 66
Total FP CONTRA 14
Total FP INCONS 34
Total FP COMP 18
Total FN 36
Total Scores
MCC 0.477
Average MCC ± 95% Confidence Intervals 0.533 ± 0.420
Sensitivity 0.520
Positive Predictive Value 0.448
Nr of predictions 4

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
2LC8_A

GP_knot1 links to Rfam database...

0.64 0.61 0.69 11 512 6 0 5 1 7
3U4M_B - 0.49 0.55 0.46 12 1250 14 3 11 0 10
4A1C_2

5_8S_rRNA links to Rfam database...

0.19 0.25 0.15 5 4483 43 11 17 15 15
4ENB_A

crcB links to Rfam database...

0.81 0.73 0.92 11 460 3 0 1 2 4

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Performance of CRWrnafold - scored lower in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP 28
Total TN 6707
Total FP 75
Total FP CONTRA 14
Total FP INCONS 43
Total FP COMP 18
Total FN 47
Total Scores
MCC 0.343
Average MCC ± 95% Confidence Intervals 0.376 ± 0.610
Sensitivity 0.373
Positive Predictive Value 0.329
Nr of predictions 4

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
2LC8_A

GP_knot1 links to Rfam database...

-0.03 0.00 0.00 0 513 15 3 12 0 18
3U4M_B - 0.49 0.55 0.46 12 1250 14 3 11 0 10
4A1C_2

5_8S_rRNA links to Rfam database...

0.19 0.25 0.15 5 4483 44 8 20 16 15
4ENB_A

crcB links to Rfam database...

0.85 0.73 1.00 11 461 2 0 0 2 4

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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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