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(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Multilign(seed)		RNAalifold(seed)
MCC	0.593	>	0.550
Average MCC ± 95% Confidence Intervals	0.567 ± 0.439	>	0.503 ± 0.362
Sensitivity	0.475	>	0.399
Positive Predictive Value	0.750	<	0.768
Total TP	75	>	63
Total TN	12928	<	12946
Total FP	26	>	20
Total FP CONTRA	2	=	2
Total FP INCONS	23	>	17
Total FP COMP	1	=	1
Total FN	83	<	95
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 RNAalifold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	63
Total TN	12946
Total FP	20
Total FP CONTRA	2
Total FP INCONS	17
Total FP COMP	1
Total FN	95

Total Scores
MCC	0.550
Average MCC ± 95% Confidence Intervals	0.503 ± 0.362
Sensitivity	0.399
Positive Predictive Value	0.768
Nr of predictions	5

2. Individual counts for RNAalifold(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...	0.59	0.40	0.89	8	981	1	0	1	0	12
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
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.