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 CRWrnafold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Multilign(seed)		CRWrnafold
MCC	0.465	>	0.443
Average MCC ± 95% Confidence Intervals	0.383 ± 0.849	>	0.367 ± 0.819
Sensitivity	0.365	<	0.375
Positive Predictive Value	0.603	>	0.534
Total TP	38	<	39
Total TN	9764	>	9754
Total FP	26	<	35
Total FP CONTRA	2	<	6
Total FP INCONS	23	<	28
Total FP COMP	1	=	1
Total FN	66	>	65
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	38
Total TN	9764
Total FP	26
Total FP CONTRA	2
Total FP INCONS	23
Total FP COMP	1
Total FN	66

Total Scores
MCC	0.465
Average MCC ± 95% Confidence Intervals	0.383 ± 0.849
Sensitivity	0.365
Positive Predictive Value	0.603
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
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	1	11	0	20
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 CRWrnafold - scored lower in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	39
Total TN	9754
Total FP	35
Total FP CONTRA	6
Total FP INCONS	28
Total FP COMP	1
Total FN	65

Total Scores
MCC	0.443
Average MCC ± 95% Confidence Intervals	0.367 ± 0.819
Sensitivity	0.375
Positive Predictive Value	0.534
Nr of predictions	3

2. Individual counts for CRWrnafold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22

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