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

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric RNAfold NanoFolder
MCC 0.452 > 0.427
Average MCC ± 95% Confidence Intervals 0.458 ± 0.227 < 0.470 ± 0.376
Sensitivity 0.481 < 0.519
Positive Predictive Value 0.439 > 0.365
Total TP 50 < 54
Total TN 8139 > 8105
Total FP 80 < 113
Total FP CONTRA 18 < 31
Total FP INCONS 46 < 63
Total FP COMP 16 < 19
Total FN 54 > 50
P-value 0.0

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Performance plots


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

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

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Performance of RNAfold - scored higher in this pairwise comparison

1. Total counts & total scores for RNAfold

Total Base Pair Counts
Total TP 50
Total TN 8139
Total FP 80
Total FP CONTRA 18
Total FP INCONS 46
Total FP COMP 16
Total FN 54
Total Scores
MCC 0.452
Average MCC ± 95% Confidence Intervals 0.458 ± 0.227
Sensitivity 0.481
Positive Predictive Value 0.439
Nr of predictions 5

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2. Individual counts for RNAfold [ 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 5 0 5 0 7
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 4482 43 11 18 14 15
4AOB_A

SAM links to Rfam database...

0.60 0.59 0.63 17 1410 11 4 6 1 12
4ENC_A

crcB links to Rfam database...

0.37 0.33 0.45 5 485 7 0 6 1 10

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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 54
Total TN 8105
Total FP 113
Total FP CONTRA 31
Total FP INCONS 63
Total FP COMP 19
Total FN 50
Total Scores
MCC 0.427
Average MCC ± 95% Confidence Intervals 0.470 ± 0.376
Sensitivity 0.519
Positive Predictive Value 0.365
Nr of predictions 5

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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
3U4M_B - 0.77 0.91 0.67 20 1246 12 6 4 2 2
4A1C_2

5_8S_rRNA links to Rfam database...

-0.01 0.00 0.00 0 4469 61 18 29 14 20
4AOB_A

SAM links to Rfam database...

0.39 0.41 0.39 12 1406 20 4 15 1 17
4ENC_A

crcB links to Rfam database...

0.66 0.73 0.61 11 478 9 2 5 2 4

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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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