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 IPknot - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

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

Overview

Metric	IPknot		Mastr(20)
MCC	0.571	>	0.567
Average MCC ± 95% Confidence Intervals	0.581 ± 0.171	>	0.510 ± 0.210
Sensitivity	0.463	>	0.389
Positive Predictive Value	0.710	<	0.833
Total TP	125	>	105
Total TN	34847	<	34897
Total FP	59	>	24
Total FP CONTRA	6	>	1
Total FP INCONS	45	>	20
Total FP COMP	8	>	3
Total FN	145	<	165
P-value	0.0

Performance plots

Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	125
Total TN	34847
Total FP	59
Total FP CONTRA	6
Total FP INCONS	45
Total FP COMP	8
Total FN	145

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.581 ± 0.171
Sensitivity	0.463
Positive Predictive Value	0.710
Nr of predictions	8

2. Individual counts for IPknot [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	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...	0.61	0.48	0.80	20	3891	5	0	5	0	22
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.52	0.42	0.67	8	1314	4	0	4	0	11

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

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

Total Base Pair Counts
Total TP	105
Total TN	34897
Total FP	24
Total FP CONTRA	1
Total FP INCONS	20
Total FP COMP	3
Total FN	165

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.510 ± 0.210
Sensitivity	0.389
Positive Predictive Value	0.833
Nr of predictions	8

2. Individual counts for Mastr(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.77	0.59	1.00	16	2987	1	0	0	1	11
3RKF_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2194	0	0	0	0	17
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	7	0	6	1	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4AOB_A	SAM links to Rfam database...	0.39	0.26	0.58	11	4352	9	0	8	1	31
4ENB_A	crcB links to Rfam database...	0.39	0.16	1.00	3	1272	0	0	0	0	16
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

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