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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric ContextFold Afold
MCC 0.646 > 0.477
Average MCC ± 95% Confidence Intervals 0.646 ± 0.485 > 0.533 ± 0.420
Sensitivity 0.600 > 0.520
Positive Predictive Value 0.703 > 0.448
Total TP 45 > 39
Total TN 6728 > 6705
Total FP 32 < 66
Total FP CONTRA 3 < 14
Total FP INCONS 16 < 34
Total FP COMP 13 < 18
Total FN 30 < 36
P-value 0.0

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Performance plots


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

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

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP 45
Total TN 6728
Total FP 32
Total FP CONTRA 3
Total FP INCONS 16
Total FP COMP 13
Total FN 30
Total Scores
MCC 0.646
Average MCC ± 95% Confidence Intervals 0.646 ± 0.485
Sensitivity 0.600
Positive Predictive Value 0.703
Nr of predictions 4

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2. Individual counts for ContextFold [ 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...

0.58 0.56 0.63 10 512 6 0 6 0 8
3U4M_B - 0.98 0.95 1.00 21 1255 0 0 0 0 1
4A1C_2

5_8S_rRNA links to Rfam database...

0.26 0.25 0.28 5 4498 26 3 10 13 15
4ENB_A

crcB links to Rfam database...

0.77 0.60 1.00 9 463 0 0 0 0 6

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Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP 39
Total TN 6705
Total FP 66
Total FP CONTRA 14
Total FP INCONS 34
Total FP COMP 18
Total FN 36
Total Scores
MCC 0.477
Average MCC ± 95% Confidence Intervals 0.533 ± 0.420
Sensitivity 0.520
Positive Predictive Value 0.448
Nr of predictions 4

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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
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 4483 43 11 17 15 15
4ENB_A

crcB links to Rfam database...

0.81 0.73 0.92 11 460 3 0 1 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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