CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Carnac(seed)
MCC	0.576	>	0.146
Average MCC ± 95% Confidence Intervals	0.566 ± 0.210	>	0.074 ± 0.191
Sensitivity	0.449	>	0.021
Positive Predictive Value	0.743	<	1.000
Total TP	84	>	4
Total TN	27320	<	27429
Total FP	43	>	0
Total FP CONTRA	2	>	0
Total FP INCONS	27	>	0
Total FP COMP	14	>	0
Total FN	103	<	183
P-value	0.0

Comparison of performance of ContextFold and Carnac(seed). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for ContextFold and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Carnac(seed). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for ContextFold and Carnac(seed)).

Total Scores
MCC	0.576
Average MCC ± 95% Confidence Intervals	0.566 ± 0.210
Sensitivity	0.449
Positive Predictive Value	0.743
Nr of predictions	6

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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.146
Average MCC ± 95% Confidence Intervals	0.074 ± 0.191
Sensitivity	0.021
Positive Predictive Value	1.000
Nr of predictions	6

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
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.