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 Multilign(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Multilign(seed)		NanoFolder
MCC	0.403	>	0.395
Average MCC ± 95% Confidence Intervals	0.299 ± 3.931	<	0.422 ± 1.212
Sensitivity	0.306	<	0.371
Positive Predictive Value	0.543	>	0.434
Total TP	19	<	23
Total TN	5876	>	5858
Total FP	17	<	31
Total FP CONTRA	1	=	1
Total FP INCONS	15	<	29
Total FP COMP	1	=	1
Total FN	43	>	39
P-value	0.0

Performance plots

Performance of Multilign(seed) - scored higher 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

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	23
Total TN	5858
Total FP	31
Total FP CONTRA	1
Total FP INCONS	29
Total FP COMP	1
Total FN	39

Total Scores
MCC	0.395
Average MCC ± 95% Confidence Intervals	0.422 ± 1.212
Sensitivity	0.371
Positive Predictive Value	0.434
Nr of predictions	2

2. Individual counts for NanoFolder [ 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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30

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