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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of PETfold_2.0(20) - scored higher in this pairwise comparison

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

  5. Compile and download dataset for PETfold_2.0(20) & IPknot [.zip] - may take several seconds...


Overview

Metric PETfold_2.0(20) IPknot
MCC 0.905 > 0.541
Average MCC ± 95% Confidence Intervals 0.905 ± > 0.541 ±
Sensitivity 0.889 > 0.556
Positive Predictive Value 0.923 > 0.536
Total TP 24 > 15
Total TN 2630 > 2628
Total FP 11 < 16
Total FP CONTRA 0 < 4
Total FP INCONS 2 < 9
Total FP COMP 9 > 3
Total FN 3 < 12
P-value 0.0

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Performance plots


  1. Comparison of performance of PETfold_2.0(20) and IPknot. 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 PETfold_2.0(20) and IPknot).

  2. Comparison of performance of PETfold_2.0(20) and IPknot. 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 PETfold_2.0(20) and IPknot).

  3. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_2.0(20) and IPknot. 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 PETfold_2.0(20) and IPknot).

  4. Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_2.0(20) and IPknot. 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 PETfold_2.0(20) and IPknot).

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Performance of PETfold_2.0(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_2.0(20)

Total Base Pair Counts
Total TP 24
Total TN 2630
Total FP 11
Total FP CONTRA 0
Total FP INCONS 2
Total FP COMP 9
Total FN 3
Total Scores
MCC 0.905
Average MCC ± 95% Confidence Intervals 0.905 ±
Sensitivity 0.889
Positive Predictive Value 0.923
Nr of predictions 1

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2. Individual counts for PETfold_2.0(20) [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
3J3V_B

5S_rRNA links to Rfam database...

0.90 0.89 0.92 24 2630 11 0 2 9 3

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Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP 15
Total TN 2628
Total FP 16
Total FP CONTRA 4
Total FP INCONS 9
Total FP COMP 3
Total FN 12
Total Scores
MCC 0.541
Average MCC ± 95% Confidence Intervals 0.541 ±
Sensitivity 0.556
Positive Predictive Value 0.536
Nr of predictions 1

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

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
3J3V_B

5S_rRNA links to Rfam database...

0.54 0.56 0.54 15 2628 16 4 9 3 12

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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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