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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 Alterna - scored lower in this pairwise comparison

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


Overview

Metric ContextFold Alterna
MCC 0.558 > 0.432
Average MCC ± 95% Confidence Intervals 0.452 ± 0.382 > 0.348 ± 0.247
Sensitivity 0.452 > 0.379
Positive Predictive Value 0.700 > 0.505
Total TP 56 > 47
Total TN 10623 > 10610
Total FP 24 < 46
Total FP CONTRA 1 < 8
Total FP INCONS 23 < 38
Total FP COMP 0 = 0
Total FN 68 < 77
P-value 0.0

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Performance plots


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

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

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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 56
Total TN 10623
Total FP 24
Total FP CONTRA 1
Total FP INCONS 23
Total FP COMP 0
Total FN 68
Total Scores
MCC 0.558
Average MCC ± 95% Confidence Intervals 0.452 ± 0.382
Sensitivity 0.452
Positive Predictive Value 0.700
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
3J0L_g - -0.01 0.00 0.00 0 462 3 1 2 0 4
3J0L_7 - -0.01 0.00 0.00 0 1212 13 0 13 0 17
3J0L_a - 0.71 0.56 0.90 9 1118 1 0 1 0 7
3J16_L

tRNA links to Rfam database...

0.75 0.57 1.00 17 2758 0 0 0 0 13
3UZL_B

tRNA links to Rfam database...

0.72 0.54 0.95 20 3549 1 0 1 0 17

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Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP 47
Total TN 10610
Total FP 46
Total FP CONTRA 8
Total FP INCONS 38
Total FP COMP 0
Total FN 77
Total Scores
MCC 0.432
Average MCC ± 95% Confidence Intervals 0.348 ± 0.247
Sensitivity 0.379
Positive Predictive Value 0.505
Nr of predictions 6

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2. Individual counts for Alterna [ 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...

0.46 0.40 0.53 8 1525 7 0 7 0 12
3J0L_g - -0.01 0.00 0.00 0 456 9 4 5 0 4
3J0L_7 - 0.26 0.24 0.31 4 1212 9 0 9 0 13
3J0L_a - 0.23 0.19 0.30 3 1118 7 1 6 0 13
3J16_L

tRNA links to Rfam database...

0.63 0.53 0.76 16 2754 5 1 4 0 14
3UZL_B

tRNA links to Rfam database...

0.52 0.43 0.64 16 3545 9 2 7 0 21

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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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