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

Home

RNA 2D Atlas

Help

FAQ

Table of contents:

Overview

Performance Plots

Performance of RNASampler(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for RNASampler(seed) & CentroidHomfold‑LAST [.zip] - may take several seconds...

Overview

Metric	RNASampler(seed)		CentroidHomfold‑LAST
MCC	0.504	>	0.496
Average MCC ± 95% Confidence Intervals	0.474 ± 0.399	<	0.487 ± 0.489
Sensitivity	0.369	<	0.403
Positive Predictive Value	0.696	>	0.619
Total TP	55	<	60
Total TN	20359	>	20341
Total FP	32	<	43
Total FP CONTRA	0	<	5
Total FP INCONS	24	<	32
Total FP COMP	8	>	6
Total FN	94	>	89
P-value	0.0

Performance plots

Performance of RNASampler(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	55
Total TN	20359
Total FP	32
Total FP CONTRA	0
Total FP INCONS	24
Total FP COMP	8
Total FN	94

Total Scores
MCC	0.504
Average MCC ± 95% Confidence Intervals	0.474 ± 0.399
Sensitivity	0.369
Positive Predictive Value	0.696
Nr of predictions	5

2. Individual counts for RNASampler(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...	0.71	0.55	0.92	11	978	1	0	1	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

Performance of CentroidHomfold‑LAST - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidHomfold‑LAST

Total Base Pair Counts
Total TP	60
Total TN	20341
Total FP	43
Total FP CONTRA	5
Total FP INCONS	32
Total FP COMP	6
Total FN	89

Total Scores
MCC	0.496
Average MCC ± 95% Confidence Intervals	0.487 ± 0.489
Sensitivity	0.403
Positive Predictive Value	0.619
Nr of predictions	5

2. Individual counts for CentroidHomfold‑LAST [ 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	1529	11	0	11	0	20
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.64	0.45	0.90	19	3895	2	0	2	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28

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