CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Alterna
MCC	0.640	>	0.568
Average MCC ± 95% Confidence Intervals	0.555 ± 0.533	>	0.507 ± 0.420
Sensitivity	0.585	>	0.549
Positive Predictive Value	0.716	>	0.608
Total TP	48	>	45
Total TN	3271	>	3264
Total FP	20	<	30
Total FP CONTRA	4	<	8
Total FP INCONS	15	<	21
Total FP COMP	1	=	1
Total FN	34	<	37
P-value	0.0

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

Total Scores
MCC	0.640
Average MCC ± 95% Confidence Intervals	0.555 ± 0.533
Sensitivity	0.585
Positive Predictive Value	0.716
Nr of predictions	4

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	1	4	0	12
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.74	0.69	0.80	20	1508	5	0	5	0	9

Total Scores
MCC	0.568
Average MCC ± 95% Confidence Intervals	0.507 ± 0.420
Sensitivity	0.549
Positive Predictive Value	0.608
Nr of predictions	4

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
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3RKF_A	Purine links to Rfam database...	0.82	0.79	0.86	19	844	3	1	2	0	5
3SD1_A	THF links to Rfam database...	0.55	0.55	0.57	16	1505	12	4	8	0	13

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