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 ContextFold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RNAalifold(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for ContextFold & RNAalifold(20) [.zip] - may take several seconds...

Overview

Metric	ContextFold		RNAalifold(20)
MCC	0.579	>	0.553
Average MCC ± 95% Confidence Intervals	0.568 ± 0.278	>	0.530 ± 0.291
Sensitivity	0.443	>	0.407
Positive Predictive Value	0.763	>	0.756
Total TP	74	>	68
Total TN	25796	<	25803
Total FP	37	>	25
Total FP CONTRA	2	=	2
Total FP INCONS	21	>	20
Total FP COMP	14	>	3
Total FN	93	<	99
P-value	0.0

Performance plots

Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	74
Total TN	25796
Total FP	37
Total FP CONTRA	2
Total FP INCONS	21
Total FP COMP	14
Total FN	93

Total Scores
MCC	0.579
Average MCC ± 95% Confidence Intervals	0.568 ± 0.278
Sensitivity	0.443
Positive Predictive Value	0.763
Nr of predictions	5

2. Individual counts for ContextFold [ 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...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Performance of RNAalifold(20) - scored lower in this pairwise comparison

1. Total counts & total scores for RNAalifold(20)

Total Base Pair Counts
Total TP	68
Total TN	25803
Total FP	25
Total FP CONTRA	2
Total FP INCONS	20
Total FP COMP	3
Total FN	99

Total Scores
MCC	0.553
Average MCC ± 95% Confidence Intervals	0.530 ± 0.291
Sensitivity	0.407
Positive Predictive Value	0.756
Nr of predictions	5

2. Individual counts for RNAalifold(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...	0.17	0.15	0.19	5	11755	23	2	19	2	28
4A1C_3	5S_rRNA links to Rfam database...	0.74	0.57	0.97	31	7108	1	0	1	0	23
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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