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Table of contents:

  1. Overview

  2. Performance Plots

  3. Performance of PETfold_2.0(seed) - 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(seed) & IPknot [.zip] - may take several seconds...


Overview

Metric PETfold_2.0(seed) IPknot
MCC 0.866 > 0.766
Average MCC ± 95% Confidence Intervals 0.868 ± 0.471 > 0.754 ± 2.708
Sensitivity 0.845 > 0.776
Positive Predictive Value 0.891 > 0.763
Total TP 49 > 45
Total TN 4279 > 4275
Total FP 19 > 17
Total FP CONTRA 2 < 5
Total FP INCONS 4 < 9
Total FP COMP 13 > 3
Total FN 9 < 13
P-value 0.0

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Performance plots


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

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

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

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

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

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

Total Base Pair Counts
Total TP 49
Total TN 4279
Total FP 19
Total FP CONTRA 2
Total FP INCONS 4
Total FP COMP 13
Total FN 9
Total Scores
MCC 0.866
Average MCC ± 95% Confidence Intervals 0.868 ± 0.471
Sensitivity 0.845
Positive Predictive Value 0.891
Nr of predictions 2

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2. Individual counts for PETfold_2.0(seed) [ 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 14 0 2 12 3
3W1K_J

tRNA-Sec links to Rfam database...

0.83 0.81 0.86 25 1649 5 2 2 1 6

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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 45
Total TN 4275
Total FP 17
Total FP CONTRA 5
Total FP INCONS 9
Total FP COMP 3
Total FN 13
Total Scores
MCC 0.766
Average MCC ± 95% Confidence Intervals 0.754 ± 2.708
Sensitivity 0.776
Positive Predictive Value 0.763
Nr of predictions 2

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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
3W1K_J

tRNA-Sec links to Rfam database...

0.97 0.97 0.97 30 1647 1 1 0 0 1

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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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