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

Overview

Metric	Afold		Multilign(seed)
MCC	0.781	>	0.610
Average MCC ± 95% Confidence Intervals	0.783 ± 0.454	>	0.558 ± 1.238
Sensitivity	0.676	>	0.500
Positive Predictive Value	0.909	>	0.755
Total TP	50	>	37
Total TN	4686	<	4692
Total FP	6	<	12
Total FP CONTRA	0	<	1
Total FP INCONS	5	<	11
Total FP COMP	1	>	0
Total FN	24	<	37
P-value	0.0

Performance plots

Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	50
Total TN	4686
Total FP	6
Total FP CONTRA	0
Total FP INCONS	5
Total FP COMP	1
Total FN	24

Total Scores
MCC	0.781
Average MCC ± 95% Confidence Intervals	0.783 ± 0.454
Sensitivity	0.676
Positive Predictive Value	0.909
Nr of predictions	3

2. Individual counts for Afold [ 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	6	0	5	1	9
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14

Performance of Multilign(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	37
Total TN	4692
Total FP	12
Total FP CONTRA	1
Total FP INCONS	11
Total FP COMP	0
Total FN	37

Total Scores
MCC	0.610
Average MCC ± 95% Confidence Intervals	0.558 ± 1.238
Sensitivity	0.500
Positive Predictive Value	0.755
Nr of predictions	3

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

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