CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RSpredict(20)		Carnac(seed)
MCC	0.581	>	0.000
Average MCC ± 95% Confidence Intervals	0.560 ± 0.193	>	0.000 ± 0.000
Sensitivity	0.511	>	0.000
Positive Predictive Value	0.672	>	0.000
Total TP	162	>	0
Total TN	24267	<	24508
Total FP	91	>	0
Total FP CONTRA	38	>	0
Total FP INCONS	41	>	0
Total FP COMP	12	>	0
Total FN	155	<	317
P-value	1.87872347734e-08

Comparison of performance of RSpredict(20) and Carnac(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 RSpredict(20) and Carnac(seed)).
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 RSpredict(20) and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RSpredict(20) and Carnac(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 RSpredict(20) and Carnac(seed)).

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.560 ± 0.193
Sensitivity	0.511
Positive Predictive Value	0.672
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3GX2_A	SAM links to Rfam database...	0.40	0.21	0.75	6	1441	2	1	1	0	22
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	1	0	0	3
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2272	6	1	5	0	37
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.30	11	4727	29	15	11	3	11
3PDR_A	ykoK links to Rfam database...	0.80	0.70	0.92	35	4802	5	1	2	2	15
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	1	0	0	3
3SD1_A	THF links to Rfam database...	0.82	0.86	0.78	25	1501	7	5	2	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4AOB_A	SAM links to Rfam database...	0.33	0.21	0.55	6	1426	5	1	4	0	23
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.51	0.40	0.67	6	487	3	0	3	0	9

Total Scores
MCC	0.000
Average MCC ± 95% Confidence Intervals	0.000 ± 0.000
Sensitivity	0.000
Positive Predictive Value	0.000
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3GX2_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1449	0	0	0	0	28
3IVN_B	Purine links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	23
3LA5_A	Purine links to Rfam database...	0.00	0.00	0.00	0	954	0	0	0	0	25
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	2278	0	0	0	0	37
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4764	0	0	0	0	22
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4840	0	0	0	0	50
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4516	0	0	0	0	20
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15

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