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 PETfold_pre2.0(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RDfolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for PETfold_pre2.0(20) & RDfolder [.zip] - may take several seconds...

Overview

Metric	PETfold_pre2.0(20)		RDfolder
MCC	0.666	>	0.387
Average MCC ± 95% Confidence Intervals	0.632 ± 0.244	>	0.403 ± 0.115
Sensitivity	0.513	>	0.288
Positive Predictive Value	0.872	>	0.535
Total TP	41	>	23
Total TN	6925	<	6929
Total FP	7	<	21
Total FP CONTRA	0	<	1
Total FP INCONS	6	<	19
Total FP COMP	1	=	1
Total FN	39	<	57
P-value	0.0

Performance plots

Performance of PETfold_pre2.0(20) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(20)

Total Base Pair Counts
Total TP	41
Total TN	6925
Total FP	7
Total FP CONTRA	0
Total FP INCONS	6
Total FP COMP	1
Total FN	39

Total Scores
MCC	0.666
Average MCC ± 95% Confidence Intervals	0.632 ± 0.244
Sensitivity	0.513
Positive Predictive Value	0.872
Nr of predictions	3

2. Individual counts for PETfold_pre2.0(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.61	0.42	0.89	8	1266	1	0	1	0	11
4ENC_A	crcB links to Rfam database...	0.55	0.42	0.73	8	1315	3	0	3	0	11

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	23
Total TN	6929
Total FP	21
Total FP CONTRA	1
Total FP INCONS	19
Total FP COMP	1
Total FN	57

Total Scores
MCC	0.387
Average MCC ± 95% Confidence Intervals	0.403 ± 0.115
Sensitivity	0.288
Positive Predictive Value	0.535
Nr of predictions	3

2. Individual counts for RDfolder [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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