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 CRWrnafold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	RNASampler(seed)		CRWrnafold
MCC	0.357	>	0.262
Average MCC ± 95% Confidence Intervals	0.299 ± 0.753	>	0.215 ± 0.685
Sensitivity	0.253	=	0.253
Positive Predictive Value	0.511	>	0.279
Total TP	24	=	24
Total TN	17190	>	17151
Total FP	31	<	71
Total FP CONTRA	0	<	8
Total FP INCONS	23	<	54
Total FP COMP	8	<	9
Total FN	71	=	71
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	24
Total TN	17190
Total FP	31
Total FP CONTRA	0
Total FP INCONS	23
Total FP COMP	8
Total FN	71

Total Scores
MCC	0.357
Average MCC ± 95% Confidence Intervals	0.299 ± 0.753
Sensitivity	0.253
Positive Predictive Value	0.511
Nr of predictions	3

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
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 CRWrnafold - scored lower in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	24
Total TN	17151
Total FP	71
Total FP CONTRA	8
Total FP INCONS	54
Total FP COMP	9
Total FN	71

Total Scores
MCC	0.262
Average MCC ± 95% Confidence Intervals	0.215 ± 0.685
Sensitivity	0.253
Positive Predictive Value	0.279
Nr of predictions	3

2. Individual counts for CRWrnafold [ 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	1525	15	2	13	0	20
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28

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