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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 0.504 > 0.475
Average MCC ± 95% Confidence Intervals 0.472 ± 0.322 > 0.454 ± 0.370
Sensitivity 0.406 < 0.442
Positive Predictive Value 0.632 > 0.518
Total TP 67 < 73
Total TN 24980 > 24945
Total FP 54 < 84
Total FP CONTRA 0 < 7
Total FP INCONS 39 < 61
Total FP COMP 15 < 16
Total FN 98 > 92
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 67
Total TN 24980
Total FP 54
Total FP CONTRA 0
Total FP INCONS 39
Total FP COMP 15
Total FN 98
Total Scores
MCC 0.504
Average MCC ± 95% Confidence Intervals 0.472 ± 0.322
Sensitivity 0.406
Positive Predictive Value 0.632
Nr of predictions 6

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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...

0.55 0.50 0.63 10 1524 6 0 6 0 10
2LKR_A - 0.65 0.56 0.76 22 6076 9 0 7 2 17
3J0L_7 - -0.01 0.00 0.00 0 1212 13 0 13 0 17
3U4M_B - 0.75 0.57 1.00 21 3139 0 0 0 0 16
4A1C_2

5_8S_rRNA links to Rfam database...

0.20 0.15 0.28 5 11763 26 0 13 13 28
4ENB_A

crcB links to Rfam database...

0.69 0.47 1.00 9 1266 0 0 0 0 10

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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 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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Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.

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