CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		NanoFolder
MCC	0.545	>	0.398
Average MCC ± 95% Confidence Intervals	0.537 ± 0.224	>	0.413 ± 0.226
Sensitivity	0.460	>	0.402
Positive Predictive Value	0.656	>	0.407
Total TP	40	>	35
Total TN	7824	>	7799
Total FP	21	<	51
Total FP CONTRA	3	<	6
Total FP INCONS	18	<	45
Total FP COMP	0	=	0
Total FN	47	<	52
P-value	0.0

Comparison of performance of Alterna and NanoFolder. 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 Alterna and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Alterna and NanoFolder. 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 Alterna and NanoFolder).

Total Scores
MCC	0.545
Average MCC ± 95% Confidence Intervals	0.537 ± 0.224
Sensitivity	0.460
Positive Predictive Value	0.656
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...	0.46	0.40	0.53	8	1525	7	0	7	0	12
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

Total Scores
MCC	0.398
Average MCC ± 95% Confidence Intervals	0.413 ± 0.226
Sensitivity	0.402
Positive Predictive Value	0.407
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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24

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