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 RNASLOpt - scored lower in this pairwise comparison

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


Overview

Metric Afold RNASLOpt
MCC 0.475 > 0.420
Average MCC ± 95% Confidence Intervals 0.454 ± 0.370 > 0.416 ± 0.300
Sensitivity 0.442 > 0.376
Positive Predictive Value 0.518 > 0.477
Total TP 73 > 62
Total TN 24945 < 24956
Total FP 84 > 75
Total FP CONTRA 7 < 8
Total FP INCONS 61 > 60
Total FP COMP 16 > 7
Total FN 92 < 103
P-value 0.0

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Performance plots


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

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

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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 73
Total TN 24945
Total FP 84
Total FP CONTRA 7
Total FP INCONS 61
Total FP COMP 16
Total FN 92
Total Scores
MCC 0.475
Average MCC ± 95% Confidence Intervals 0.454 ± 0.370
Sensitivity 0.442
Positive Predictive Value 0.518
Nr of predictions 6

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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...

0.61 0.55 0.69 11 1524 6 0 5 1 9
2LKR_A - 0.93 0.87 1.00 34 6071 3 0 0 3 5
3J0L_7 - -0.01 0.00 0.00 0 1210 15 1 14 0 17
3U4M_B - 0.38 0.32 0.46 12 3134 14 0 14 0 25
4A1C_2

5_8S_rRNA links to Rfam database...

0.14 0.15 0.14 5 11745 43 5 26 12 28
4ENB_A

crcB links to Rfam database...

0.67 0.58 0.79 11 1261 3 1 2 0 8

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Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP 62
Total TN 24956
Total FP 75
Total FP CONTRA 8
Total FP INCONS 60
Total FP COMP 7
Total FN 103
Total Scores
MCC 0.420
Average MCC ± 95% Confidence Intervals 0.416 ± 0.300
Sensitivity 0.376
Positive Predictive Value 0.477
Nr of predictions 6

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2. Individual counts for RNASLOpt [ 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 0.35 0.64 7 1529 4 0 4 0 13
2LKR_A - 0.68 0.62 0.75 24 6073 9 0 8 1 15
3J0L_7 - -0.01 0.00 0.00 0 1212 13 0 13 0 17
3U4M_B - 0.38 0.32 0.46 12 3134 14 0 14 0 25
4A1C_2

5_8S_rRNA links to Rfam database...

0.23 0.24 0.22 8 11744 35 8 21 6 25
4ENB_A

crcB links to Rfam database...

0.76 0.58 1.00 11 1264 0 0 0 0 8

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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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