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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 Contrafold - scored lower in this pairwise comparison

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


Overview

Metric PETfold_2.0(seed) Contrafold
MCC 0.769 > 0.649
Average MCC ± 95% Confidence Intervals 0.771 ± 0.133 > 0.678 ± 2.482
Sensitivity 0.642 > 0.547
Positive Predictive Value 0.924 > 0.776
Total TP 61 > 52
Total TN 11141 > 11140
Total FP 7 < 15
Total FP CONTRA 1 < 2
Total FP INCONS 4 < 13
Total FP COMP 2 > 0
Total FN 34 < 43
P-value 0.0

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Performance plots


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

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

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

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

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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 61
Total TN 11141
Total FP 7
Total FP CONTRA 1
Total FP INCONS 4
Total FP COMP 2
Total FN 34
Total Scores
MCC 0.769
Average MCC ± 95% Confidence Intervals 0.771 ± 0.133
Sensitivity 0.642
Positive Predictive Value 0.924
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...

0.76 0.61 0.95 35 6984 3 0 2 1 22
3W1K_J

tRNA-Sec links to Rfam database...

0.78 0.68 0.90 26 4157 4 1 2 1 12

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Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP 52
Total TN 11140
Total FP 15
Total FP CONTRA 2
Total FP INCONS 13
Total FP COMP 0
Total FN 43
Total Scores
MCC 0.649
Average MCC ± 95% Confidence Intervals 0.678 ± 2.482
Sensitivity 0.547
Positive Predictive Value 0.776
Nr of predictions 2

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2. Individual counts for Contrafold [ 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...

0.48 0.39 0.61 22 6985 14 1 13 0 35
3W1K_J

tRNA-Sec links to Rfam database...

0.87 0.79 0.97 30 4155 1 1 0 0 8

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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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