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 PPfold(20) - 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 PPfold(20) & Carnac(seed) [.zip] - may take several seconds...

Overview

Metric	PPfold(20)		Carnac(seed)
MCC	0.641	>	0.268
Average MCC ± 95% Confidence Intervals	0.612 ± 0.150	>	0.122 ± 0.288
Sensitivity	0.490	>	0.072
Positive Predictive Value	0.843	<	1.000
Total TP	129	>	19
Total TN	32857	<	32991
Total FP	29	>	0
Total FP CONTRA	0	=	0
Total FP INCONS	24	>	0
Total FP COMP	5	>	0
Total FN	134	<	244
P-value	0.0

Performance plots

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

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

Total Base Pair Counts
Total TP	129
Total TN	32857
Total FP	29
Total FP CONTRA	0
Total FP INCONS	24
Total FP COMP	5
Total FN	134

Total Scores
MCC	0.641
Average MCC ± 95% Confidence Intervals	0.612 ± 0.150
Sensitivity	0.490
Positive Predictive Value	0.843
Nr of predictions	8

2. Individual counts for PPfold(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...	0.63	0.45	0.90	9	980	1	0	1	0	11
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	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	19
Total TN	32991
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	244

Total Scores
MCC	0.268
Average MCC ± 95% Confidence Intervals	0.122 ± 0.288
Sensitivity	0.072
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
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
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_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
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.