CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidAlifold(20)		Alterna
MCC	0.775	>	0.537
Average MCC ± 95% Confidence Intervals	0.775 ± 0.066	>	0.546 ± 0.164
Sensitivity	0.635	>	0.465
Positive Predictive Value	0.952	>	0.630
Total TP	198	>	145
Total TN	29600	>	29578
Total FP	15	<	93
Total FP CONTRA	6	<	11
Total FP INCONS	4	<	74
Total FP COMP	5	<	8
Total FN	114	<	167
P-value	6.48923495589e-09

Comparison of performance of CentroidAlifold(20) 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 CentroidAlifold(20) 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 CentroidAlifold(20) and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) 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 CentroidAlifold(20) and Alterna).

Total Scores
MCC	0.775
Average MCC ± 95% Confidence Intervals	0.775 ± 0.066
Sensitivity	0.635
Positive Predictive Value	0.952
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3GX2_A	SAM links to Rfam database...	0.77	0.60	1.00	24	4347	1	0	0	1	16
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.71	0.52	0.96	22	3893	1	0	1	0	20

Total Scores
MCC	0.537
Average MCC ± 95% Confidence Intervals	0.546 ± 0.164
Sensitivity	0.465
Positive Predictive Value	0.630
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XQD_Y	tRNA links to Rfam database...	0.67	0.59	0.76	16	2829	5	0	5	0	11
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
3IVN_B	Purine links to Rfam database...	0.74	0.61	0.90	19	2325	2	1	1	0	12
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	0	22	0	32
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
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

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