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 Carnac(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	IPknot		Carnac(20)
MCC	0.571	>	0.560
Average MCC ± 95% Confidence Intervals	0.581 ± 0.171	>	0.442 ± 0.254
Sensitivity	0.463	>	0.367
Positive Predictive Value	0.710	<	0.861
Total TP	125	>	99
Total TN	34847	<	34908
Total FP	59	>	20
Total FP CONTRA	6	>	1
Total FP INCONS	45	>	15
Total FP COMP	8	>	4
Total FN	145	<	171
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 Carnac(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	99
Total TN	34908
Total FP	20
Total FP CONTRA	1
Total FP INCONS	15
Total FP COMP	4
Total FN	171

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.442 ± 0.254
Sensitivity	0.367
Positive Predictive Value	0.861
Nr of predictions	8

2. Individual counts for Carnac(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...	0.69	0.59	0.80	16	2983	6	0	4	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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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