CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	MXScarna(20)		Afold
MCC	0.645	>	0.547
Average MCC ± 95% Confidence Intervals	0.629 ± 0.182	>	0.562 ± 0.223
Sensitivity	0.597	>	0.579
Positive Predictive Value	0.701	>	0.524
Total TP	190	>	184
Total TN	44979	>	44899
Total FP	125	<	221
Total FP CONTRA	41	<	57
Total FP INCONS	40	<	110
Total FP COMP	44	<	54
Total FN	128	<	134
P-value	1.52299983238e-08

Comparison of performance of MXScarna(20) and Afold. 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 MXScarna(20) and Afold).
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 MXScarna(20) and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and Afold. 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 MXScarna(20) and Afold).

Total Scores
MCC	0.645
Average MCC ± 95% Confidence Intervals	0.629 ± 0.182
Sensitivity	0.597
Positive Predictive Value	0.701
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.74	0.73	0.76	16	1087	6	1	4	1	6
3IVN_B	Purine links to Rfam database...	0.81	0.74	0.89	17	884	2	2	0	0	6
3IZ4_A	tmRNA links to Rfam database...	0.58	0.54	0.63	51	25455	35	18	12	5	44
3J3E_8	5_8S_rRNA links to Rfam database...	0.21	0.20	0.23	3	2729	15	4	6	5	12
3JYV_7	tRNA links to Rfam database...	0.95	0.90	1.00	18	1093	2	0	0	2	2
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	9	2	4	3	10
3O58_3	5_8S_rRNA links to Rfam database...	0.62	0.59	0.65	13	4744	18	5	2	11	9
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13

Total Scores
MCC	0.547
Average MCC ± 95% Confidence Intervals	0.562 ± 0.223
Sensitivity	0.579
Positive Predictive Value	0.524
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

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