CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		Alterna
MCC	0.812	>	0.648
Average MCC ± 95% Confidence Intervals	0.782 ± 0.801	>	0.637 ± 0.370
Sensitivity	0.745	>	0.655
Positive Predictive Value	0.891	>	0.655
Total TP	41	>	36
Total TN	2934	>	2925
Total FP	14	<	25
Total FP CONTRA	0	<	7
Total FP INCONS	5	<	12
Total FP COMP	9	>	6
Total FN	14	<	19
P-value	0.0

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

Total Scores
MCC	0.812
Average MCC ± 95% Confidence Intervals	0.782 ± 0.801
Sensitivity	0.745
Positive Predictive Value	0.891
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
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	1	0	0	1	0
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	8	0	0	8	2

Total Scores
MCC	0.648
Average MCC ± 95% Confidence Intervals	0.637 ± 0.370
Sensitivity	0.655
Positive Predictive Value	0.655
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...	0.47	0.44	0.53	8	513	7	0	7	0	10
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	3	2	0	5
3UZL_B	tRNA links to Rfam database...	0.68	0.75	0.63	12	1274	13	4	3	6	4

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