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 RNAwolf - scored lower in this pairwise comparison

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


Overview

Metric Afold RNAwolf
MCC 0.567 > 0.491
Average MCC ± 95% Confidence Intervals 0.609 ± 0.353 > 0.496 ± 0.339
Sensitivity 0.596 > 0.495
Positive Predictive Value 0.551 > 0.500
Total TP 59 > 49
Total TN 7551 < 7560
Total FP 66 > 63
Total FP CONTRA 14 = 14
Total FP INCONS 34 < 35
Total FP COMP 18 > 14
Total FN 40 < 50
P-value 0.0

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Performance plots


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

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

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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 59
Total TN 7551
Total FP 66
Total FP CONTRA 14
Total FP INCONS 34
Total FP COMP 18
Total FN 40
Total Scores
MCC 0.567
Average MCC ± 95% Confidence Intervals 0.609 ± 0.353
Sensitivity 0.596
Positive Predictive Value 0.551
Nr of predictions 5

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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
3RKF_A

Purine links to Rfam database...

0.91 0.83 1.00 20 846 0 0 0 0 4
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 RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP 49
Total TN 7560
Total FP 63
Total FP CONTRA 14
Total FP INCONS 35
Total FP COMP 14
Total FN 50
Total Scores
MCC 0.491
Average MCC ± 95% Confidence Intervals 0.496 ± 0.339
Sensitivity 0.495
Positive Predictive Value 0.500
Nr of predictions 5

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2. Individual counts for RNAwolf [ 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...

0.52 0.50 0.56 9 512 7 0 7 0 9
3RKF_A

Purine links to Rfam database...

0.89 0.83 0.95 20 845 1 0 1 0 4
3U4M_B - 0.50 0.50 0.52 11 1255 12 1 9 2 11
4A1C_2

5_8S_rRNA links to Rfam database...

0.12 0.15 0.10 3 4487 38 12 14 12 17
4ENB_A

crcB links to Rfam database...

0.45 0.40 0.55 6 461 5 1 4 0 9

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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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