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

Overview

Metric	PknotsRG		Multilign(seed)
MCC	0.667	>	0.593
Average MCC ± 95% Confidence Intervals	0.696 ± 0.225	>	0.567 ± 0.439
Sensitivity	0.557	>	0.475
Positive Predictive Value	0.807	>	0.750
Total TP	88	>	75
Total TN	12919	<	12928
Total FP	22	<	26
Total FP CONTRA	4	>	2
Total FP INCONS	17	<	23
Total FP COMP	1	=	1
Total FN	70	<	83
P-value	0.0

Performance plots

Performance of PknotsRG - scored higher in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	88
Total TN	12919
Total FP	22
Total FP CONTRA	4
Total FP INCONS	17
Total FP COMP	1
Total FN	70

Total Scores
MCC	0.667
Average MCC ± 95% Confidence Intervals	0.696 ± 0.225
Sensitivity	0.557
Positive Predictive Value	0.807
Nr of predictions	5

2. Individual counts for PknotsRG [ 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...	0.63	0.55	0.73	11	1525	4	1	3	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...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25

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.