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(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	RNASampler(seed)		PPfold(seed)
MCC	0.471	>	0.169
Average MCC ± 95% Confidence Intervals	0.415 ± 0.540	>	0.137 ± 0.359
Sensitivity	0.341	>	0.054
Positive Predictive Value	0.657	>	0.538
Total TP	44	>	7
Total TN	19381	<	19435
Total FP	31	>	25
Total FP CONTRA	0	=	0
Total FP INCONS	23	>	6
Total FP COMP	8	<	19
Total FN	85	<	122
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	44
Total TN	19381
Total FP	31
Total FP CONTRA	0
Total FP INCONS	23
Total FP COMP	8
Total FN	85

Total Scores
MCC	0.471
Average MCC ± 95% Confidence Intervals	0.415 ± 0.540
Sensitivity	0.341
Positive Predictive Value	0.657
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
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
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(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	7
Total TN	19435
Total FP	25
Total FP CONTRA	0
Total FP INCONS	6
Total FP COMP	19
Total FN	122

Total Scores
MCC	0.169
Average MCC ± 95% Confidence Intervals	0.137 ± 0.359
Sensitivity	0.054
Positive Predictive Value	0.538
Nr of predictions	4

2. Individual counts for PPfold(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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32

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