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 Murlet(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Murlet(seed)		NanoFolder
MCC	0.403	>	0.280
Average MCC ± 95% Confidence Intervals	0.396 ± 0.439	>	0.354 ± 0.414
Sensitivity	0.237	<	0.298
Positive Predictive Value	0.692	>	0.272
Total TP	27	<	34
Total TN	18979	>	18893
Total FP	13	<	101
Total FP CONTRA	0	<	13
Total FP INCONS	12	<	78
Total FP COMP	1	<	10
Total FN	87	>	80
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	27
Total TN	18979
Total FP	13
Total FP CONTRA	0
Total FP INCONS	12
Total FP COMP	1
Total FN	87

Total Scores
MCC	0.403
Average MCC ± 95% Confidence Intervals	0.396 ± 0.439
Sensitivity	0.237
Positive Predictive Value	0.692
Nr of predictions	4

2. Individual counts for Murlet(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	0	12	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	34
Total TN	18893
Total FP	101
Total FP CONTRA	13
Total FP INCONS	78
Total FP COMP	10
Total FN	80

Total Scores
MCC	0.280
Average MCC ± 95% Confidence Intervals	0.354 ± 0.414
Sensitivity	0.298
Positive Predictive Value	0.272
Nr of predictions	4

2. Individual counts for NanoFolder [ 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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

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