CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of ContextFold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

Compile and download dataset for ContextFold & Multilign(seed) [.zip] - may take several seconds...

Overview

Metric	ContextFold		Multilign(seed)
MCC	0.532	>	0.403
Average MCC ± 95% Confidence Intervals	0.538 ± 0.208	>	0.299 ± 3.931
Sensitivity	0.435	>	0.306
Positive Predictive Value	0.659	>	0.543
Total TP	27	>	19
Total TN	5870	<	5876
Total FP	15	<	17
Total FP CONTRA	1	=	1
Total FP INCONS	13	<	15
Total FP COMP	1	=	1
Total FN	35	<	43
P-value	0.0

Performance plots

Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	27
Total TN	5870
Total FP	15
Total FP CONTRA	1
Total FP INCONS	13
Total FP COMP	1
Total FN	35

Total Scores
MCC	0.532
Average MCC ± 95% Confidence Intervals	0.538 ± 0.208
Sensitivity	0.435
Positive Predictive Value	0.659
Nr of predictions	2

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.55	0.50	0.63	10	1524	6	0	6	0	10
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25

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

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

Total Base Pair Counts
Total TP	19
Total TN	5876
Total FP	17
Total FP CONTRA	1
Total FP INCONS	15
Total FP COMP	1
Total FN	43

Total Scores
MCC	0.403
Average MCC ± 95% Confidence Intervals	0.299 ± 3.931
Sensitivity	0.306
Positive Predictive Value	0.543
Nr of predictions	2

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.