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 RNASampler(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 RNASampler(seed) & NanoFolder [.zip] - may take several seconds...

Overview

Metric	RNASampler(seed)		NanoFolder
MCC	0.198	>	0.171
Average MCC ± 95% Confidence Intervals	0.150 ± 2.027	<	0.257 ± 3.313
Sensitivity	0.151	<	0.208
Positive Predictive Value	0.267	>	0.147
Total TP	8	<	11
Total TN	13291	>	13246
Total FP	30	<	72
Total FP CONTRA	0	<	12
Total FP INCONS	22	<	52
Total FP COMP	8	=	8
Total FN	45	>	42
P-value	0.0

Performance plots

Performance of RNASampler(seed) - scored higher 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

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	11
Total TN	13246
Total FP	72
Total FP CONTRA	12
Total FP INCONS	52
Total FP COMP	8
Total FN	42

Total Scores
MCC	0.171
Average MCC ± 95% Confidence Intervals	0.257 ± 3.313
Sensitivity	0.208
Positive Predictive Value	0.147
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33

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