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

Overview

Metric	CRWrnafold		Carnac(seed)
MCC	0.483	>	0.132
Average MCC ± 95% Confidence Intervals	0.476 ± 0.272	>	0.064 ± 0.156
Sensitivity	0.428	>	0.017
Positive Predictive Value	0.554	<	1.000
Total TP	98	>	4
Total TN	31172	<	31345
Total FP	89	>	0
Total FP CONTRA	12	>	0
Total FP INCONS	67	>	0
Total FP COMP	10	>	0
Total FN	131	<	225
P-value	0.0

Performance plots

Performance of CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	98
Total TN	31172
Total FP	89
Total FP CONTRA	12
Total FP INCONS	67
Total FP COMP	10
Total FN	131

Total Scores
MCC	0.483
Average MCC ± 95% Confidence Intervals	0.476 ± 0.272
Sensitivity	0.428
Positive Predictive Value	0.554
Nr of predictions	7

2. Individual counts for CRWrnafold [ 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...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

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	31345
Total FP	0
Total FP CONTRA	0
Total FP INCONS	0
Total FP COMP	0
Total FN	225

Total Scores
MCC	0.132
Average MCC ± 95% Confidence Intervals	0.064 ± 0.156
Sensitivity	0.017
Positive Predictive Value	1.000
Nr of predictions	7

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
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.