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(seed) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	IPknot		Carnac(seed)
MCC	0.544	>	0.123
Average MCC ± 95% Confidence Intervals	0.543 ± 0.173	>	0.056 ± 0.132
Sensitivity	0.437	>	0.015
Positive Predictive Value	0.685	<	1.000
Total TP	115	>	4
Total TN	33392	<	33556
Total FP	59	>	0
Total FP CONTRA	7	>	0
Total FP INCONS	46	>	0
Total FP COMP	6	>	0
Total FN	148	<	259
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	115
Total TN	33392
Total FP	59
Total FP CONTRA	7
Total FP INCONS	46
Total FP COMP	6
Total FN	148

Total Scores
MCC	0.544
Average MCC ± 95% Confidence Intervals	0.543 ± 0.173
Sensitivity	0.437
Positive Predictive Value	0.685
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
2LC8_A	GP_knot1 links to Rfam database...	0.40	0.30	0.55	6	1529	5	1	4	0	14
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(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	4
Total TN	33556
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	259

Total Scores
MCC	0.123
Average MCC ± 95% Confidence Intervals	0.056 ± 0.132
Sensitivity	0.015
Positive Predictive Value	1.000
Nr of predictions	8

2. Individual counts for Carnac(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.20	1.00	4	1536	0	0	0	0	16
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
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...	0.00	0.00	0.00	0	4371	0	0	0	0	42
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.