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

Overview

Metric	Afold		Multilign(20)
MCC	0.503	>	0.412
Average MCC ± 95% Confidence Intervals	0.579 ± 0.414	>	0.444 ± 0.514
Sensitivity	0.459	>	0.338
Positive Predictive Value	0.557	>	0.510
Total TP	68	>	50
Total TN	21286	<	21310
Total FP	66	>	52
Total FP CONTRA	7	>	5
Total FP INCONS	47	>	43
Total FP COMP	12	>	4
Total FN	80	<	98
P-value	0.0

Performance plots

Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	68
Total TN	21286
Total FP	66
Total FP CONTRA	7
Total FP INCONS	47
Total FP COMP	12
Total FN	80

Total Scores
MCC	0.503
Average MCC ± 95% Confidence Intervals	0.579 ± 0.414
Sensitivity	0.459
Positive Predictive Value	0.557
Nr of predictions	5

2. Individual counts for Afold [ 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...	0.34	0.31	0.39	13	5118	20	1	19	0	29
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

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

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

Total Base Pair Counts
Total TP	50
Total TN	21310
Total FP	52
Total FP CONTRA	5
Total FP INCONS	43
Total FP COMP	4
Total FN	98

Total Scores
MCC	0.412
Average MCC ± 95% Confidence Intervals	0.444 ± 0.514
Sensitivity	0.338
Positive Predictive Value	0.510
Nr of predictions	5

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
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4ENB_A	crcB links to Rfam database...	0.34	0.26	0.45	5	1264	6	1	5	0	14

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