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 RNASampler(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	RNASampler(seed)		PPfold(20)
MCC	0.581	>	0.569
Average MCC ± 95% Confidence Intervals	0.594 ± 0.321	>	0.561 ± 0.378
Sensitivity	0.426	=	0.426
Positive Predictive Value	0.797	>	0.764
Total TP	55	=	55
Total TN	18829	>	18826
Total FP	22	>	21
Total FP CONTRA	0	=	0
Total FP INCONS	14	<	17
Total FP COMP	8	>	4
Total FN	74	=	74
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	55
Total TN	18829
Total FP	22
Total FP CONTRA	0
Total FP INCONS	14
Total FP COMP	8
Total FN	74

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.594 ± 0.321
Sensitivity	0.426
Positive Predictive Value	0.797
Nr of predictions	4

2. Individual counts for RNASampler(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...	0.71	0.55	0.92	11	978	1	0	1	0	9
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

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

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

Total Base Pair Counts
Total TP	55
Total TN	18826
Total FP	21
Total FP CONTRA	0
Total FP INCONS	17
Total FP COMP	4
Total FN	74

Total Scores
MCC	0.569
Average MCC ± 95% Confidence Intervals	0.561 ± 0.378
Sensitivity	0.426
Positive Predictive Value	0.764
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
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28

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