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

Overview

Metric	Cylofold		Multilign(20)
MCC	0.577	>	0.546
Average MCC ± 95% Confidence Intervals	0.652 ± 0.248	>	0.551 ± 0.244
Sensitivity	0.494	>	0.429
Positive Predictive Value	0.684	<	0.705
Total TP	121	>	105
Total TN	22066	<	22094
Total FP	59	>	47
Total FP CONTRA	3	<	5
Total FP INCONS	53	>	39
Total FP COMP	3	=	3
Total FN	124	<	140
P-value	0.0

Performance plots

Performance of Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	121
Total TN	22066
Total FP	59
Total FP CONTRA	3
Total FP INCONS	53
Total FP COMP	3
Total FN	124

Total Scores
MCC	0.577
Average MCC ± 95% Confidence Intervals	0.652 ± 0.248
Sensitivity	0.494
Positive Predictive Value	0.684
Nr of predictions	8

2. Individual counts for Cylofold [ 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...	0.10	0.10	0.11	4	5115	32	1	31	0	38
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
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...	0.62	0.50	0.78	21	3889	6	0	6	0	21
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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

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

Total Base Pair Counts
Total TP	105
Total TN	22094
Total FP	47
Total FP CONTRA	5
Total FP INCONS	39
Total FP COMP	3
Total FN	140

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.551 ± 0.244
Sensitivity	0.429
Positive Predictive Value	0.705
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
3AMU_B	tRNA links to Rfam database...	0.63	0.56	0.71	15	2982	8	0	6	2	12
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
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.