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 Murlet(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	Murlet(seed)		PETfold_pre2.0(20)
MCC	0.539	>	0.527
Average MCC ± 95% Confidence Intervals	0.538 ± 0.084	>	0.523 ± 0.372
Sensitivity	0.292	<	0.407
Positive Predictive Value	1.000	>	0.687
Total TP	33	<	46
Total TN	18720	>	18686
Total FP	1	<	32
Total FP CONTRA	0	=	0
Total FP INCONS	0	<	21
Total FP COMP	1	<	11
Total FN	80	>	67
P-value	0.0

Performance plots

Performance of Murlet(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	33
Total TN	18720
Total FP	1
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	1
Total FN	80

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.538 ± 0.084
Sensitivity	0.292
Positive Predictive Value	1.000
Nr of predictions	4

2. Individual counts for Murlet(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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

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

Total Base Pair Counts
Total TP	46
Total TN	18686
Total FP	32
Total FP CONTRA	0
Total FP INCONS	21
Total FP COMP	11
Total FN	67

Total Scores
MCC	0.527
Average MCC ± 95% Confidence Intervals	0.523 ± 0.372
Sensitivity	0.407
Positive Predictive Value	0.687
Nr of predictions	4

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
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.15	0.25	5	11761	25	0	15	10	28
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

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