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Table of contents:

  1. Overview

  2. Performance Plots

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

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

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


Overview

Metric ProbKnot Cylofold
MCC 0.634 > 0.271
Average MCC ± 95% Confidence Intervals 0.628 ± 0.889 > 0.275 ± 1.303
Sensitivity 0.620 > 0.241
Positive Predictive Value 0.649 > 0.308
Total TP 85 > 33
Total TN 60457 < 60481
Total FP 62 < 78
Total FP CONTRA 4 > 3
Total FP INCONS 42 < 71
Total FP COMP 16 > 4
Total FN 52 < 104
P-value 0.0

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Performance plots


  1. Comparison of performance of ProbKnot and Cylofold. 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 ProbKnot and Cylofold).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and Cylofold. 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 ProbKnot and Cylofold).

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP 85
Total TN 60457
Total FP 62
Total FP CONTRA 4
Total FP INCONS 42
Total FP COMP 16
Total FN 52
Total Scores
MCC 0.634
Average MCC ± 95% Confidence Intervals 0.628 ± 0.889
Sensitivity 0.620
Positive Predictive Value 0.649
Nr of predictions 2

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2. Individual counts for ProbKnot [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
ASE_00408 - 0.70 0.72 0.68 51 32310 31 4 20 7 20
ASE_00429 - 0.56 0.52 0.61 34 28147 31 0 22 9 32

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Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP 33
Total TN 60481
Total FP 78
Total FP CONTRA 3
Total FP INCONS 71
Total FP COMP 4
Total FN 104
Total Scores
MCC 0.271
Average MCC ± 95% Confidence Intervals 0.275 ± 1.303
Sensitivity 0.241
Positive Predictive Value 0.308
Nr of predictions 2

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2. Individual counts for Cylofold [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
ASE_00408 - 0.17 0.15 0.20 11 32329 45 3 42 0 60
ASE_00429 - 0.38 0.33 0.43 22 28152 33 0 29 4 44

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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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