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 RNAsubopt - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Multilign(seed)		RNAsubopt
MCC	0.593	>	0.588
Average MCC ± 95% Confidence Intervals	0.567 ± 0.439	<	0.572 ± 0.457
Sensitivity	0.475	<	0.494
Positive Predictive Value	0.750	>	0.709
Total TP	75	<	78
Total TN	12928	>	12918
Total FP	26	<	33
Total FP CONTRA	2	<	5
Total FP INCONS	23	<	27
Total FP COMP	1	=	1
Total FN	83	>	80
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	75
Total TN	12928
Total FP	26
Total FP CONTRA	2
Total FP INCONS	23
Total FP COMP	1
Total FN	83

Total Scores
MCC	0.593
Average MCC ± 95% Confidence Intervals	0.567 ± 0.439
Sensitivity	0.475
Positive Predictive Value	0.750
Nr of predictions	5

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
2L94_A	HIV_FE links to Rfam database...	0.92	0.85	1.00	17	973	0	0	0	0	3
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.55	0.45	0.68	19	3888	9	1	8	0	23
4AOB_A	SAM links to Rfam database...	0.61	0.45	0.83	19	4348	5	0	4	1	23

Performance of RNAsubopt - scored lower in this pairwise comparison

1. Total counts & total scores for RNAsubopt

Total Base Pair Counts
Total TP	78
Total TN	12918
Total FP	33
Total FP CONTRA	5
Total FP INCONS	27
Total FP COMP	1
Total FN	80

Total Scores
MCC	0.588
Average MCC ± 95% Confidence Intervals	0.572 ± 0.457
Sensitivity	0.494
Positive Predictive Value	0.709
Nr of predictions	5

2. Individual counts for RNAsubopt [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24

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