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

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Fold Alterna
MCC 0.589 > 0.560
Average MCC ± 95% Confidence Intervals 0.497 ± 0.405 < 0.511 ± 0.227
Sensitivity 0.582 > 0.552
Positive Predictive Value 0.614 > 0.587
Total TP 78 > 74
Total TN 5765 < 5766
Total FP 50 < 53
Total FP CONTRA 15 > 12
Total FP INCONS 34 < 40
Total FP COMP 1 = 1
Total FN 56 < 60
P-value 0.0

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Performance plots


  1. Comparison of performance of Fold and Alterna. 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 Fold and Alterna).

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

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP 78
Total TN 5765
Total FP 50
Total FP CONTRA 15
Total FP INCONS 34
Total FP COMP 1
Total FN 56
Total Scores
MCC 0.589
Average MCC ± 95% Confidence Intervals 0.497 ± 0.405
Sensitivity 0.582
Positive Predictive Value 0.614
Nr of predictions 6

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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
2LC8_A

GP_knot1 links to Rfam database...

-0.03 0.00 0.00 0 513 15 3 12 0 18
3ADB_C - 0.86 0.85 0.88 28 1787 4 0 4 0 5
3J0L_a - 0.15 0.18 0.17 2 399 11 4 6 1 9
3NKB_B - 0.41 0.42 0.42 8 716 11 4 7 0 11
3RKF_A

Purine links to Rfam database...

0.91 0.83 1.00 20 846 0 0 0 0 4
3SD1_A

THF links to Rfam database...

0.68 0.69 0.69 20 1504 9 4 5 0 9

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Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP 74
Total TN 5766
Total FP 53
Total FP CONTRA 12
Total FP INCONS 40
Total FP COMP 1
Total FN 60
Total Scores
MCC 0.560
Average MCC ± 95% Confidence Intervals 0.511 ± 0.227
Sensitivity 0.552
Positive Predictive Value 0.587
Nr of predictions 6

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2. Individual counts for Alterna [ 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...

0.47 0.44 0.53 8 513 7 0 7 0 10
3ADB_C - 0.63 0.64 0.64 21 1786 12 1 11 0 12
3J0L_a - 0.18 0.18 0.22 2 402 8 3 4 1 9
3NKB_B - 0.41 0.42 0.42 8 716 11 3 8 0 11
3RKF_A

Purine links to Rfam database...

0.82 0.79 0.86 19 844 3 1 2 0 5
3SD1_A

THF links to Rfam database...

0.55 0.55 0.57 16 1505 12 4 8 0 13

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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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