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 TurboFold(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Alterna - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	TurboFold(20)		Alterna
MCC	0.721	>	0.654
Average MCC ± 95% Confidence Intervals	0.745 ± 0.220	>	0.692 ± 0.338
Sensitivity	0.602	>	0.569
Positive Predictive Value	0.871	>	0.761
Total TP	74	>	70
Total TN	10035	>	10028
Total FP	13	<	24
Total FP CONTRA	1	<	2
Total FP INCONS	10	<	20
Total FP COMP	2	=	2
Total FN	49	<	53
P-value	0.0

Performance plots

Performance of TurboFold(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	74
Total TN	10035
Total FP	13
Total FP CONTRA	1
Total FP INCONS	10
Total FP COMP	2
Total FN	49

Total Scores
MCC	0.721
Average MCC ± 95% Confidence Intervals	0.745 ± 0.220
Sensitivity	0.602
Positive Predictive Value	0.871
Nr of predictions	4

2. Individual counts for TurboFold(20) [ 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
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.59	0.48	0.74	20	3889	7	1	6	0	22

Performance of Alterna - scored lower in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	70
Total TN	10028
Total FP	24
Total FP CONTRA	2
Total FP INCONS	20
Total FP COMP	2
Total FN	53

Total Scores
MCC	0.654
Average MCC ± 95% Confidence Intervals	0.692 ± 0.338
Sensitivity	0.569
Positive Predictive Value	0.761
Nr of predictions	4

2. Individual counts for Alterna [ 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
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

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