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(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Afold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	PETfold_pre2.0(seed)		Afold
MCC	0.508	>	0.389
Average MCC ± 95% Confidence Intervals	0.490 ± 0.213	>	0.474 ± 0.718
Sensitivity	0.403	>	0.375
Positive Predictive Value	0.644	>	0.409
Total TP	29	>	27
Total TN	14551	>	14530
Total FP	22	<	52
Total FP CONTRA	1	<	6
Total FP INCONS	15	<	33
Total FP COMP	6	<	13
Total FN	43	<	45
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	29
Total TN	14551
Total FP	22
Total FP CONTRA	1
Total FP INCONS	15
Total FP COMP	6
Total FN	43

Total Scores
MCC	0.508
Average MCC ± 95% Confidence Intervals	0.490 ± 0.213
Sensitivity	0.403
Positive Predictive Value	0.644
Nr of predictions	3

2. Individual counts for PETfold_pre2.0(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...	0.40	0.30	0.55	6	1529	5	0	5	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4ENB_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1262	5	1	4	0	11

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	27
Total TN	14530
Total FP	52
Total FP CONTRA	6
Total FP INCONS	33
Total FP COMP	13
Total FN	45

Total Scores
MCC	0.389
Average MCC ± 95% Confidence Intervals	0.474 ± 0.718
Sensitivity	0.375
Positive Predictive Value	0.409
Nr of predictions	3

2. Individual counts for Afold [ 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...	0.61	0.55	0.69	11	1524	6	0	5	1	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

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