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

Overview

Metric	Pknots		Multilign(seed)
MCC	0.607	>	0.593
Average MCC ± 95% Confidence Intervals	0.659 ± 0.361	>	0.567 ± 0.439
Sensitivity	0.519	>	0.475
Positive Predictive Value	0.719	<	0.750
Total TP	82	>	75
Total TN	12914	<	12928
Total FP	33	>	26
Total FP CONTRA	2	=	2
Total FP INCONS	30	>	23
Total FP COMP	1	=	1
Total FN	76	<	83
P-value	0.0

Performance plots

Performance of Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	82
Total TN	12914
Total FP	33
Total FP CONTRA	2
Total FP INCONS	30
Total FP COMP	1
Total FN	76

Total Scores
MCC	0.607
Average MCC ± 95% Confidence Intervals	0.659 ± 0.361
Sensitivity	0.519
Positive Predictive Value	0.719
Nr of predictions	5

2. Individual counts for Pknots [ 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	0.90	0.95	18	971	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.79	0.75	0.83	15	1522	3	1	2	0	5
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.65	0.52	0.81	22	3889	5	0	5	0	20
4AOB_A	SAM links to Rfam database...	0.17	0.14	0.21	6	4343	23	1	21	1	36

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.