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 Alterna - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of NanoFolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for Alterna & NanoFolder [.zip] - may take several seconds...

Overview

Metric	Alterna		NanoFolder
MCC	0.654	>	0.539
Average MCC ± 95% Confidence Intervals	0.729 ± 0.228	>	0.674 ± 0.307
Sensitivity	0.567	>	0.533
Positive Predictive Value	0.764	>	0.557
Total TP	68	>	64
Total TN	8829	>	8803
Total FP	22	<	52
Total FP CONTRA	3	<	6
Total FP INCONS	18	<	45
Total FP COMP	1	=	1
Total FN	52	<	56
P-value	0.0

Performance plots

Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	68
Total TN	8829
Total FP	22
Total FP CONTRA	3
Total FP INCONS	18
Total FP COMP	1
Total FN	52

Total Scores
MCC	0.654
Average MCC ± 95% Confidence Intervals	0.729 ± 0.228
Sensitivity	0.567
Positive Predictive Value	0.764
Nr of predictions	6

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
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	64
Total TN	8803
Total FP	52
Total FP CONTRA	6
Total FP INCONS	45
Total FP COMP	1
Total FN	56

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.674 ± 0.307
Sensitivity	0.533
Positive Predictive Value	0.557
Nr of predictions	6

2. Individual counts for NanoFolder [ 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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24

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