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 McQFold - 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 McQFold & Multilign(seed) [.zip] - may take several seconds...

Overview

Metric	McQFold		Multilign(seed)
MCC	0.672	>	0.593
Average MCC ± 95% Confidence Intervals	0.696 ± 0.253	>	0.567 ± 0.439
Sensitivity	0.563	>	0.475
Positive Predictive Value	0.809	>	0.750
Total TP	89	>	75
Total TN	12918	<	12928
Total FP	22	<	26
Total FP CONTRA	1	<	2
Total FP INCONS	20	<	23
Total FP COMP	1	=	1
Total FN	69	<	83
P-value	0.0

Performance plots

Performance of McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	89
Total TN	12918
Total FP	22
Total FP CONTRA	1
Total FP INCONS	20
Total FP COMP	1
Total FN	69

Total Scores
MCC	0.672
Average MCC ± 95% Confidence Intervals	0.696 ± 0.253
Sensitivity	0.563
Positive Predictive Value	0.809
Nr of predictions	5

2. Individual counts for McQFold [ 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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
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...	0.71	0.60	0.86	25	3887	4	0	4	0	17
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28

Performance of Multilign(seed) - scored lower 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

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