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 RNAalifold(seed) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of Multilign(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for RNAalifold(seed) & Multilign(20) [.zip] - may take several seconds...

Overview

Metric	RNAalifold(seed)		Multilign(20)
MCC	0.572	>	0.468
Average MCC ± 95% Confidence Intervals	0.561 ± 0.084	>	0.491 ± 0.269
Sensitivity	0.355	<	0.378
Positive Predictive Value	0.927	>	0.586
Total TP	89	<	95
Total TN	30925	>	30859
Total FP	10	<	72
Total FP CONTRA	2	<	8
Total FP INCONS	5	<	59
Total FP COMP	3	<	5
Total FN	162	>	156
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	89
Total TN	30925
Total FP	10
Total FP CONTRA	2
Total FP INCONS	5
Total FP COMP	3
Total FN	162

Total Scores
MCC	0.572
Average MCC ± 95% Confidence Intervals	0.561 ± 0.084
Sensitivity	0.355
Positive Predictive Value	0.927
Nr of predictions	8

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
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	9	5142	0	0	0	0	33
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
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

Performance of Multilign(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	95
Total TN	30859
Total FP	72
Total FP CONTRA	8
Total FP INCONS	59
Total FP COMP	5
Total FN	156

Total Scores
MCC	0.468
Average MCC ± 95% Confidence Intervals	0.491 ± 0.269
Sensitivity	0.378
Positive Predictive Value	0.586
Nr of predictions	8

2. Individual counts for Multilign(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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5139	12	1	11	0	42
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	1	8	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4AOB_A	SAM links to Rfam database...	0.49	0.38	0.64	16	4346	10	1	8	1	26
4ENB_A	crcB links to Rfam database...	0.34	0.26	0.45	5	1264	6	1	5	0	14
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

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