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(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	ContextFold		RNAalifold(seed)
MCC	0.488	>	0.472
Average MCC ± 95% Confidence Intervals	0.523 ± 0.237	>	0.444 ± 0.347
Sensitivity	0.376	>	0.293
Positive Predictive Value	0.641	<	0.765
Total TP	50	>	39
Total TN	20215	<	20242
Total FP	42	>	15
Total FP CONTRA	2	>	0
Total FP INCONS	26	>	12
Total FP COMP	14	>	3
Total FN	83	<	94
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	50
Total TN	20215
Total FP	42
Total FP CONTRA	2
Total FP INCONS	26
Total FP COMP	14
Total FN	83

Total Scores
MCC	0.488
Average MCC ± 95% Confidence Intervals	0.523 ± 0.237
Sensitivity	0.376
Positive Predictive Value	0.641
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
2LC8_A	GP_knot1 links to Rfam database...	0.55	0.50	0.63	10	1524	6	0	6	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
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(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	39
Total TN	20242
Total FP	15
Total FP CONTRA	0
Total FP INCONS	12
Total FP COMP	3
Total FN	94

Total Scores
MCC	0.472
Average MCC ± 95% Confidence Intervals	0.444 ± 0.347
Sensitivity	0.293
Positive Predictive Value	0.765
Nr of predictions	5

2. Individual counts for RNAalifold(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	1528	12	0	12	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
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...	0.56	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

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