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 PPfold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Alterna - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PPfold(20) & Alterna [.zip] - may take several seconds...

Overview

Metric	PPfold(20)		Alterna
MCC	0.726	>	0.654
Average MCC ± 95% Confidence Intervals	0.723 ± 0.157	>	0.692 ± 0.338
Sensitivity	0.569	=	0.569
Positive Predictive Value	0.933	>	0.761
Total TP	70	=	70
Total TN	10045	>	10028
Total FP	6	<	24
Total FP CONTRA	0	<	2
Total FP INCONS	5	<	20
Total FP COMP	1	<	2
Total FN	53	=	53
P-value	0.0

Performance plots

Performance of PPfold(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	70
Total TN	10045
Total FP	6
Total FP CONTRA	0
Total FP INCONS	5
Total FP COMP	1
Total FN	53

Total Scores
MCC	0.726
Average MCC ± 95% Confidence Intervals	0.723 ± 0.157
Sensitivity	0.569
Positive Predictive Value	0.933
Nr of predictions	4

2. Individual counts for PPfold(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...	0.63	0.45	0.90	9	980	1	0	1	0	11
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20

Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	70
Total TN	10028
Total FP	24
Total FP CONTRA	2
Total FP INCONS	20
Total FP COMP	2
Total FN	53

Total Scores
MCC	0.654
Average MCC ± 95% Confidence Intervals	0.692 ± 0.338
Sensitivity	0.569
Positive Predictive Value	0.761
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
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
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

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