CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		Afold
MCC	0.627	>	0.469
Average MCC ± 95% Confidence Intervals	0.605 ± 0.470	>	0.547 ± 0.800
Sensitivity	0.547	>	0.509
Positive Predictive Value	0.725	>	0.443
Total TP	29	>	27
Total TN	5476	>	5455
Total FP	22	<	52
Total FP CONTRA	2	<	11
Total FP INCONS	9	<	23
Total FP COMP	11	<	18
Total FN	24	<	26
P-value	0.0

Comparison of performance of PETfold_pre2.0(seed) and Afold. 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 PETfold_pre2.0(seed) and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Afold. 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 PETfold_pre2.0(seed) and Afold).

Total Scores
MCC	0.627
Average MCC ± 95% Confidence Intervals	0.605 ± 0.470
Sensitivity	0.547
Positive Predictive Value	0.725
Nr of predictions	3

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...	0.41	0.33	0.55	6	517	5	0	5	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
4ENB_A	crcB links to Rfam database...	0.61	0.53	0.73	8	461	5	1	2	2	7

Total Scores
MCC	0.469
Average MCC ± 95% Confidence Intervals	0.547 ± 0.800
Sensitivity	0.509
Positive Predictive Value	0.443
Nr of predictions	3

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

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