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 Multilign(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RDfolder - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Multilign(20)		RDfolder
MCC	0.626	>	0.478
Average MCC ± 95% Confidence Intervals	0.631 ± 0.187	>	0.488 ± 0.260
Sensitivity	0.517	>	0.360
Positive Predictive Value	0.766	>	0.646
Total TP	105	>	73
Total TN	16955	<	16979
Total FP	35	<	43
Total FP CONTRA	4	>	3
Total FP INCONS	28	<	37
Total FP COMP	3	=	3
Total FN	98	<	130
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	105
Total TN	16955
Total FP	35
Total FP CONTRA	4
Total FP INCONS	28
Total FP COMP	3
Total FN	98

Total Scores
MCC	0.626
Average MCC ± 95% Confidence Intervals	0.631 ± 0.187
Sensitivity	0.517
Positive Predictive Value	0.766
Nr of predictions	7

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
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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	73
Total TN	16979
Total FP	43
Total FP CONTRA	3
Total FP INCONS	37
Total FP COMP	3
Total FN	130

Total Scores
MCC	0.478
Average MCC ± 95% Confidence Intervals	0.488 ± 0.260
Sensitivity	0.360
Positive Predictive Value	0.646
Nr of predictions	7

2. Individual counts for RDfolder [ 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
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
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...	0.30	0.17	0.54	7	3903	6	0	6	0	35
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...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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