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 Multilign(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PETfold_pre2.0(seed) & Multilign(seed) [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(seed)		Multilign(seed)
MCC	0.623	>	0.403
Average MCC ± 95% Confidence Intervals	0.562 ± 2.067	>	0.299 ± 3.931
Sensitivity	0.484	>	0.306
Positive Predictive Value	0.811	>	0.543
Total TP	30	>	19
Total TN	5874	<	5876
Total FP	8	<	17
Total FP CONTRA	0	<	1
Total FP INCONS	7	<	15
Total FP COMP	1	=	1
Total FN	32	<	43
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	30
Total TN	5874
Total FP	8
Total FP CONTRA	0
Total FP INCONS	7
Total FP COMP	1
Total FN	32

Total Scores
MCC	0.623
Average MCC ± 95% Confidence Intervals	0.562 ± 2.067
Sensitivity	0.484
Positive Predictive Value	0.811
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
4AOB_A	SAM links to Rfam database...	0.72	0.57	0.92	24	4345	3	0	2	1	18

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.