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 Afold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of TurboFold(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Afold		TurboFold(seed)
MCC	0.571	>	0.470
Average MCC ± 95% Confidence Intervals	0.632 ± 0.381	>	0.502 ± 0.507
Sensitivity	0.524	>	0.413
Positive Predictive Value	0.629	>	0.542
Total TP	66	>	52
Total TN	17692	<	17701
Total FP	52	<	53
Total FP CONTRA	6	>	5
Total FP INCONS	33	<	39
Total FP COMP	13	>	9
Total FN	60	<	74
P-value	0.0

Performance plots

Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	66
Total TN	17692
Total FP	52
Total FP CONTRA	6
Total FP INCONS	33
Total FP COMP	13
Total FN	60

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.632 ± 0.381
Sensitivity	0.524
Positive Predictive Value	0.629
Nr of predictions	5

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
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	6	0	5	1	9
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
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

Performance of TurboFold(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	52
Total TN	17701
Total FP	53
Total FP CONTRA	5
Total FP INCONS	39
Total FP COMP	9
Total FN	74

Total Scores
MCC	0.470
Average MCC ± 95% Confidence Intervals	0.502 ± 0.507
Sensitivity	0.413
Positive Predictive Value	0.542
Nr of predictions	5

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10

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