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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 HotKnots - scored lower in this pairwise comparison

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


Overview

Metric PETfold_2.0(20) HotKnots
MCC 0.647 > 0.541
Average MCC ± 95% Confidence Intervals 0.647 ± > 0.541 ±
Sensitivity 0.509 > 0.439
Positive Predictive Value 0.829 > 0.676
Total TP 29 > 25
Total TN 6986 > 6984
Total FP 6 < 12
Total FP CONTRA 1 = 1
Total FP INCONS 5 < 11
Total FP COMP 0 = 0
Total FN 28 < 32
P-value 0.0

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Performance plots


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

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

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

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

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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 29
Total TN 6986
Total FP 6
Total FP CONTRA 1
Total FP INCONS 5
Total FP COMP 0
Total FN 28
Total Scores
MCC 0.647
Average MCC ± 95% Confidence Intervals 0.647 ±
Sensitivity 0.509
Positive Predictive Value 0.829
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...

0.65 0.51 0.83 29 6986 6 1 5 0 28

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Performance of HotKnots - scored lower in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP 25
Total TN 6984
Total FP 12
Total FP CONTRA 1
Total FP INCONS 11
Total FP COMP 0
Total FN 32
Total Scores
MCC 0.541
Average MCC ± 95% Confidence Intervals 0.541 ±
Sensitivity 0.439
Positive Predictive Value 0.676
Nr of predictions 1

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2. Individual counts for HotKnots [ 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 0.44 0.68 25 6984 12 1 11 0 32

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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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