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 Murlet(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 Murlet(seed) & Multilign(20) [.zip] - may take several seconds...

Overview

Metric	Murlet(seed)		Multilign(20)
MCC	0.505	>	0.468
Average MCC ± 95% Confidence Intervals	0.515 ± 0.062	>	0.491 ± 0.269
Sensitivity	0.279	<	0.378
Positive Predictive Value	0.921	>	0.586
Total TP	70	<	95
Total TN	30945	>	30859
Total FP	7	<	72
Total FP CONTRA	1	<	8
Total FP INCONS	5	<	59
Total FP COMP	1	<	5
Total FN	181	>	156
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	70
Total TN	30945
Total FP	7
Total FP CONTRA	1
Total FP INCONS	5
Total FP COMP	1
Total FN	181

Total Scores
MCC	0.505
Average MCC ± 95% Confidence Intervals	0.515 ± 0.062
Sensitivity	0.279
Positive Predictive Value	0.921
Nr of predictions	8

2. Individual counts for Murlet(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...	0.38	0.14	1.00	6	5145	0	0	0	0	36
3RKF_A	Purine links to Rfam database...	0.53	0.35	0.80	12	2196	3	1	2	0	22
3SD1_A	THF links to Rfam database...	0.47	0.26	0.85	11	3903	2	0	2	0	31
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
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.