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 NanoFolder - scored lower in this pairwise comparison

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


Overview

Metric Afold NanoFolder
MCC 0.765 > 0.610
Average MCC ± 95% Confidence Intervals 0.844 ± 0.169 > 0.789 ± 0.219
Sensitivity 0.798 > 0.711
Positive Predictive Value 0.742 > 0.537
Total TP 138 > 123
Total TN 9852 > 9809
Total FP 77 < 131
Total FP CONTRA 14 < 40
Total FP INCONS 34 < 66
Total FP COMP 29 > 25
Total FN 35 < 50
P-value 2.04409141234e-08

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Performance plots


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

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

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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 138
Total TN 9852
Total FP 77
Total FP CONTRA 14
Total FP INCONS 34
Total FP COMP 29
Total FN 35
Total Scores
MCC 0.765
Average MCC ± 95% Confidence Intervals 0.844 ± 0.169
Sensitivity 0.798
Positive Predictive Value 0.742
Nr of predictions 12

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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
2LDL_A - 1.00 1.00 1.00 9 131 1 0 0 1 0
2LI4_A - 1.00 1.00 1.00 14 175 0 0 0 0 0
2LK3_A - 1.00 1.00 1.00 9 91 0 0 0 0 0
2LKR_A - 1.00 1.00 1.00 29 2411 8 0 0 8 0
2LQZ_A - 1.00 1.00 1.00 8 124 2 0 0 2 0
2LWK_A - 0.85 0.82 0.90 9 197 2 0 1 1 2
3SN2_B

IRE_II links to Rfam database...

0.95 0.92 1.00 11 143 0 0 0 0 1
3U4M_B - 0.49 0.55 0.46 12 1250 14 3 11 0 10
3VJR_D - 1.00 1.00 1.00 12 239 1 0 0 1 0
4A1C_2

5_8S_rRNA links to Rfam database...

0.19 0.25 0.15 5 4483 43 11 17 15 15
4A4U_A - 1.00 1.00 1.00 9 96 0 0 0 0 0

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Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP 123
Total TN 9809
Total FP 131
Total FP CONTRA 40
Total FP INCONS 66
Total FP COMP 25
Total FN 50
Total Scores
MCC 0.610
Average MCC ± 95% Confidence Intervals 0.789 ± 0.219
Sensitivity 0.711
Positive Predictive Value 0.537
Nr of predictions 12

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2. Individual counts for NanoFolder [ 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...

0.54 0.61 0.50 11 506 11 1 10 0 7
2LDL_A - 1.00 1.00 1.00 9 131 1 0 0 1 0
2LI4_A - 1.00 1.00 1.00 14 175 0 0 0 0 0
2LK3_A - 1.00 1.00 1.00 9 91 0 0 0 0 0
2LKR_A - 0.26 0.34 0.21 10 2392 41 15 23 3 19
2LQZ_A - 1.00 1.00 1.00 8 124 3 0 0 3 0
2LWK_A - 0.95 0.91 1.00 10 197 2 0 0 2 1
3SN2_B

IRE_II links to Rfam database...

0.95 0.92 1.00 11 143 0 0 0 0 1
3U4M_B - 0.77 0.91 0.67 20 1246 12 6 4 2 2
3VJR_D - 1.00 1.00 1.00 12 239 0 0 0 0 0
4A1C_2

5_8S_rRNA links to Rfam database...

-0.01 0.00 0.00 0 4469 61 18 29 14 20
4A4U_A - 1.00 1.00 1.00 9 96 0 0 0 0 0

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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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