CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		RNASampler(seed)
MCC	0.667	>	0.644
Average MCC ± 95% Confidence Intervals	0.690 ± 0.210	>	0.630 ± 0.351
Sensitivity	0.560	>	0.474
Positive Predictive Value	0.803	<	0.883
Total TP	98	>	83
Total TN	13952	<	13980
Total FP	24	>	11
Total FP CONTRA	3	>	0
Total FP INCONS	21	>	11
Total FP COMP	0	=	0
Total FN	77	<	92
P-value	0.0

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

Total Scores
MCC	0.667
Average MCC ± 95% Confidence Intervals	0.690 ± 0.210
Sensitivity	0.560
Positive Predictive Value	0.803
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.70	1.00	26	3629	0	0	0	0	11
3IVN_B	Purine links to Rfam database...	0.74	0.61	0.90	19	2325	2	1	1	0	12
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26

Total Scores
MCC	0.644
Average MCC ± 95% Confidence Intervals	0.630 ± 0.351
Sensitivity	0.474
Positive Predictive Value	0.883
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.70	0.49	1.00	18	3637	0	0	0	0	19
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26

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