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Table of contents:

  1. Overview

  2. Performance Plots

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

  4. Performance of Carnac(seed) - scored lower in this pairwise comparison

  5. Compile and download dataset for IPknot & Carnac(seed) [.zip] - may take several seconds...


Overview

Metric IPknot Carnac(seed)
MCC 0.825 > 0.729
Average MCC ± 95% Confidence Intervals 0.825 ± > 0.729 ±
Sensitivity 0.769 > 0.570
Positive Predictive Value 0.887 < 0.932
Total TP 352 > 261
Total TN 1085204 < 1085321
Total FP 78 > 35
Total FP CONTRA 4 < 6
Total FP INCONS 41 > 13
Total FP COMP 33 > 16
Total FN 106 < 197
P-value 0.0

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Performance plots


  1. Comparison of performance of IPknot and Carnac(seed). 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 IPknot and Carnac(seed)).

  2. Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and Carnac(seed). 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 IPknot and Carnac(seed)).

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP 352
Total TN 1085204
Total FP 78
Total FP CONTRA 4
Total FP INCONS 41
Total FP COMP 33
Total FN 106
Total Scores
MCC 0.825
Average MCC ± 95% Confidence Intervals 0.825 ±
Sensitivity 0.769
Positive Predictive Value 0.887
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
CRW_00024

SSU_rRNA_archaea links to Rfam database...

0.83 0.77 0.89 352 1085204 78 4 41 33 106

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Performance of Carnac(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for Carnac(seed)

Total Base Pair Counts
Total TP 261
Total TN 1085321
Total FP 35
Total FP CONTRA 6
Total FP INCONS 13
Total FP COMP 16
Total FN 197
Total Scores
MCC 0.729
Average MCC ± 95% Confidence Intervals 0.729 ±
Sensitivity 0.570
Positive Predictive Value 0.932
Nr of predictions 1

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2. Individual counts for Carnac(seed) [ download as .csv ]

RNA Chain Rfam family MCC SENS PPV TP TN FP FP CONTRA FP INCONS FP COMP FN
CRW_00024

SSU_rRNA_archaea links to Rfam database...

0.73 0.57 0.93 261 1085321 35 6 13 16 197

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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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