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 RNASLOpt - 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 RNASLOpt & RNASampler(seed) [.zip] - may take several seconds...

Overview

Metric	RNASLOpt		RNASampler(seed)
MCC	0.295	>	0.198
Average MCC ± 95% Confidence Intervals	0.347 ± 1.527	>	0.150 ± 2.027
Sensitivity	0.283	>	0.151
Positive Predictive Value	0.313	>	0.267
Total TP	15	>	8
Total TN	13273	<	13291
Total FP	39	>	30
Total FP CONTRA	8	>	0
Total FP INCONS	25	>	22
Total FP COMP	6	<	8
Total FN	38	<	45
P-value	0.0

Performance plots

Performance of RNASLOpt - scored higher in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	15
Total TN	13273
Total FP	39
Total FP CONTRA	8
Total FP INCONS	25
Total FP COMP	6
Total FN	38

Total Scores
MCC	0.295
Average MCC ± 95% Confidence Intervals	0.347 ± 1.527
Sensitivity	0.283
Positive Predictive Value	0.313
Nr of predictions	2

2. Individual counts for RNASLOpt [ 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	0.35	0.64	7	1529	4	0	4	0	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25

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

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

Total Base Pair Counts
Total TP	8
Total TN	13291
Total FP	30
Total FP CONTRA	0
Total FP INCONS	22
Total FP COMP	8
Total FN	45

Total Scores
MCC	0.198
Average MCC ± 95% Confidence Intervals	0.150 ± 2.027
Sensitivity	0.151
Positive Predictive Value	0.267
Nr of predictions	2

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
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.