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 RNAalifold(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for Multilign(seed) & RNAalifold(20) [.zip] - may take several seconds...

Overview

Metric	Multilign(seed)		RNAalifold(20)
MCC	0.678	>	0.672
Average MCC ± 95% Confidence Intervals	0.711 ± 0.265	>	0.660 ± 0.137
Sensitivity	0.543	>	0.536
Positive Predictive Value	0.852	>	0.851
Total TP	75	>	74
Total TN	11400	<	11401
Total FP	14	=	14
Total FP CONTRA	1	=	1
Total FP INCONS	12	=	12
Total FP COMP	1	=	1
Total FN	63	<	64
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	11400
Total FP	14
Total FP CONTRA	1
Total FP INCONS	12
Total FP COMP	1
Total FN	63

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.711 ± 0.265
Sensitivity	0.543
Positive Predictive Value	0.852
Nr of predictions	4

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
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 RNAalifold(20) - scored lower in this pairwise comparison

1. Total counts & total scores for RNAalifold(20)

Total Base Pair Counts
Total TP	74
Total TN	11401
Total FP	14
Total FP CONTRA	1
Total FP INCONS	12
Total FP COMP	1
Total FN	64

Total Scores
MCC	0.672
Average MCC ± 95% Confidence Intervals	0.660 ± 0.137
Sensitivity	0.536
Positive Predictive Value	0.851
Nr of predictions	4

2. Individual counts for RNAalifold(20) [ 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...	0.53	0.50	0.59	10	973	7	0	7	0	10
3RKF_A	Purine links to Rfam database...	0.68	0.50	0.94	17	2193	1	0	1	0	17
3SD1_A	THF links to Rfam database...	0.70	0.60	0.83	25	3886	5	1	4	0	17
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20

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