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

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric Alterna CRWrnafold
MCC 0.462 > 0.394
Average MCC ± 95% Confidence Intervals 0.402 ± 0.485 > 0.328 ± 0.827
Sensitivity 0.448 > 0.397
Positive Predictive Value 0.500 > 0.418
Total TP 26 > 23
Total TN 2420 > 2417
Total FP 27 < 33
Total FP CONTRA 7 < 12
Total FP INCONS 19 < 20
Total FP COMP 1 = 1
Total FN 32 < 35
P-value 0.0

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Performance plots


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

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

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Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP 26
Total TN 2420
Total FP 27
Total FP CONTRA 7
Total FP INCONS 19
Total FP COMP 1
Total FN 32
Total Scores
MCC 0.462
Average MCC ± 95% Confidence Intervals 0.402 ± 0.485
Sensitivity 0.448
Positive Predictive Value 0.500
Nr of predictions 3

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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
3J0L_a - 0.18 0.18 0.22 2 402 8 3 4 1 9
3SD1_A

THF links to Rfam database...

0.55 0.55 0.57 16 1505 12 4 8 0 13

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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 23
Total TN 2417
Total FP 33
Total FP CONTRA 12
Total FP INCONS 20
Total FP COMP 1
Total FN 35
Total Scores
MCC 0.394
Average MCC ± 95% Confidence Intervals 0.328 ± 0.827
Sensitivity 0.397
Positive Predictive Value 0.418
Nr of predictions 3

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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
3J0L_a - 0.39 0.36 0.44 4 402 6 3 2 1 7
3SD1_A

THF links to Rfam database...

0.63 0.66 0.61 19 1502 12 6 6 0 10

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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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