CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		Alterna
MCC	0.586	>	0.522
Average MCC ± 95% Confidence Intervals	0.526 ± 0.176	>	0.484 ± 0.123
Sensitivity	0.529	>	0.455
Positive Predictive Value	0.659	>	0.609
Total TP	201	>	173
Total TN	31826	<	31847
Total FP	107	<	113
Total FP CONTRA	15	=	15
Total FP INCONS	89	<	96
Total FP COMP	3	>	2
Total FN	179	<	207
P-value	2.50323628132e-08

Comparison of performance of ProbKnot 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 ProbKnot and Alterna).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for ProbKnot and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot 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 ProbKnot and Alterna).

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.526 ± 0.176
Sensitivity	0.529
Positive Predictive Value	0.659
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.45	0.32	0.67	6	621	3	0	3	0	13
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2XQD_Y	tRNA links to Rfam database...	0.90	0.81	1.00	22	2828	1	0	0	1	5
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AM1_B	-	0.74	0.71	0.78	25	3208	7	1	6	0	10
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3J0L_a	-	0.55	0.50	0.62	8	1115	5	2	3	0	8
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_g	-	-0.01	0.00	0.00	0	458	7	2	5	0	4
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
3UZL_B	tRNA links to Rfam database...	0.73	0.62	0.85	23	3543	4	0	4	0	14

Total Scores
MCC	0.522
Average MCC ± 95% Confidence Intervals	0.484 ± 0.123
Sensitivity	0.455
Positive Predictive Value	0.609
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2XQD_Y	tRNA links to Rfam database...	0.67	0.59	0.76	16	2829	5	0	5	0	11
3AKZ_H	tRNA links to Rfam database...	0.40	0.39	0.42	11	2675	15	4	11	0	17
3AM1_B	-	0.61	0.57	0.67	20	3210	10	1	9	0	15
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3NKB_B	-	0.35	0.31	0.42	8	1997	11	0	11	0	18
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
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

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