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 Multilign(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Mastr(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for Multilign(seed) & Mastr(20) [.zip] - may take several seconds...

Overview

Metric	Multilign(seed)		Mastr(20)
MCC	0.678	>	0.611
Average MCC ± 95% Confidence Intervals	0.711 ± 0.265	>	0.641 ± 0.319
Sensitivity	0.543	>	0.471
Positive Predictive Value	0.852	>	0.802
Total TP	75	>	65
Total TN	11400	<	11407
Total FP	14	<	17
Total FP CONTRA	1	=	1
Total FP INCONS	12	<	15
Total FP COMP	1	=	1
Total FN	63	<	73
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	75
Total TN	11400
Total FP	14
Total FP CONTRA	1
Total FP INCONS	12
Total FP COMP	1
Total FN	63

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.711 ± 0.265
Sensitivity	0.543
Positive Predictive Value	0.852
Nr of predictions	4

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
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

Performance of Mastr(20) - scored lower in this pairwise comparison

1. Total counts & total scores for Mastr(20)

Total Base Pair Counts
Total TP	65
Total TN	11407
Total FP	17
Total FP CONTRA	1
Total FP INCONS	15
Total FP COMP	1
Total FN	73

Total Scores
MCC	0.611
Average MCC ± 95% Confidence Intervals	0.641 ± 0.319
Sensitivity	0.471
Positive Predictive Value	0.802
Nr of predictions	4

2. Individual counts for Mastr(20) [ 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...	0.87	0.80	0.94	16	973	1	0	1	0	4
3RKF_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2194	0	0	0	0	17
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...	0.39	0.26	0.58	11	4352	9	0	8	1	31

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