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 IPknot - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	IPknot		RNASampler(seed)
MCC	0.493	>	0.471
Average MCC ± 95% Confidence Intervals	0.487 ± 0.413	>	0.415 ± 0.540
Sensitivity	0.395	>	0.341
Positive Predictive Value	0.622	<	0.657
Total TP	51	>	44
Total TN	19366	<	19381
Total FP	36	>	31
Total FP CONTRA	5	>	0
Total FP INCONS	26	>	23
Total FP COMP	5	<	8
Total FN	78	<	85
P-value	0.0

Performance plots

Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	51
Total TN	19366
Total FP	36
Total FP CONTRA	5
Total FP INCONS	26
Total FP COMP	5
Total FN	78

Total Scores
MCC	0.493
Average MCC ± 95% Confidence Intervals	0.487 ± 0.413
Sensitivity	0.395
Positive Predictive Value	0.622
Nr of predictions	4

2. Individual counts for IPknot [ 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...	0.40	0.30	0.55	6	1529	5	1	4	0	14
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...	0.61	0.48	0.80	20	3891	5	0	5	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28

Performance of RNASampler(seed) - scored lower 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

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