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 PETfold_pre2.0(seed) - 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 PETfold_pre2.0(seed) & RNASampler(seed) [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(seed)		RNASampler(seed)
MCC	0.508	>	0.198
Average MCC ± 95% Confidence Intervals	0.484 ± 1.080	>	0.150 ± 2.027
Sensitivity	0.396	>	0.151
Positive Predictive Value	0.656	>	0.267
Total TP	21	>	8
Total TN	13289	<	13291
Total FP	17	<	30
Total FP CONTRA	0	=	0
Total FP INCONS	11	<	22
Total FP COMP	6	<	8
Total FN	32	<	45
P-value	0.0

Performance plots

Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

Total Base Pair Counts
Total TP	21
Total TN	13289
Total FP	17
Total FP CONTRA	0
Total FP INCONS	11
Total FP COMP	6
Total FN	32

Total Scores
MCC	0.508
Average MCC ± 95% Confidence Intervals	0.484 ± 1.080
Sensitivity	0.396
Positive Predictive Value	0.656
Nr of predictions	2

2. Individual counts for PETfold_pre2.0(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...	0.40	0.30	0.55	6	1529	5	0	5	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18

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.