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 RNASampler(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	ContextFold		RNASampler(seed)
MCC	0.351	>	0.198
Average MCC ± 95% Confidence Intervals	0.379 ± 2.226	>	0.150 ± 2.027
Sensitivity	0.283	>	0.151
Positive Predictive Value	0.441	>	0.267
Total TP	15	>	8
Total TN	13287	<	13291
Total FP	32	>	30
Total FP CONTRA	0	=	0
Total FP INCONS	19	<	22
Total FP COMP	13	>	8
Total FN	38	<	45
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	15
Total TN	13287
Total FP	32
Total FP CONTRA	0
Total FP INCONS	19
Total FP COMP	13
Total FN	38

Total Scores
MCC	0.351
Average MCC ± 95% Confidence Intervals	0.379 ± 2.226
Sensitivity	0.283
Positive Predictive Value	0.441
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28

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

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

Total Base Pair Counts
Total TP	8
Total TN	13291
Total FP	30
Total FP CONTRA	0
Total FP INCONS	22
Total FP COMP	8
Total FN	45

Total Scores
MCC	0.198
Average MCC ± 95% Confidence Intervals	0.150 ± 2.027
Sensitivity	0.151
Positive Predictive Value	0.267
Nr of predictions	2

2. Individual counts for RNASampler(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	1530	10	0	10	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

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