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 Alterna - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	Alterna		TurboFold(seed)
MCC	0.624	>	0.594
Average MCC ± 95% Confidence Intervals	0.646 ± 0.390	>	0.566 ± 0.650
Sensitivity	0.534	>	0.500
Positive Predictive Value	0.738	>	0.716
Total TP	62	>	58
Total TN	8573	<	8576
Total FP	22	<	23
Total FP CONTRA	2	<	3
Total FP INCONS	20	=	20
Total FP COMP	0	=	0
Total FN	54	<	58
P-value	0.0

Performance plots

Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	62
Total TN	8573
Total FP	22
Total FP CONTRA	2
Total FP INCONS	20
Total FP COMP	0
Total FN	54

Total Scores
MCC	0.624
Average MCC ± 95% Confidence Intervals	0.646 ± 0.390
Sensitivity	0.534
Positive Predictive Value	0.738
Nr of predictions	4

2. Individual counts for Alterna [ 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...	0.46	0.40	0.53	8	1525	7	0	7	0	12
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

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

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

Total Base Pair Counts
Total TP	58
Total TN	8576
Total FP	23
Total FP CONTRA	3
Total FP INCONS	20
Total FP COMP	0
Total FN	58

Total Scores
MCC	0.594
Average MCC ± 95% Confidence Intervals	0.566 ± 0.650
Sensitivity	0.500
Positive Predictive Value	0.716
Nr of predictions	4

2. Individual counts for TurboFold(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	0.90	0.95	18	971	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	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...	0.59	0.48	0.74	20	3889	7	1	6	0	22

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