CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(20)		Vsfold5
MCC	0.703	>	0.495
Average MCC ± 95% Confidence Intervals	0.698 ± 0.114	>	0.538 ± 0.201
Sensitivity	0.659	>	0.480
Positive Predictive Value	0.755	>	0.519
Total TP	299	>	218
Total TN	51867	>	51843
Total FP	147	<	242
Total FP CONTRA	49	<	52
Total FP INCONS	48	<	150
Total FP COMP	50	>	40
Total FN	155	<	236
P-value	2.71568867205e-08

Comparison of performance of MXScarna(20) and Vsfold5. 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 Vsfold5).
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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and Vsfold5. 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 Vsfold5).

Total Scores
MCC	0.703
Average MCC ± 95% Confidence Intervals	0.698 ± 0.114
Sensitivity	0.659
Positive Predictive Value	0.755
Nr of predictions	15

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
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	6	2	2	2	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
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
3PDR_A	ykoK links to Rfam database...	0.85	0.82	0.89	41	4794	9	2	3	4	9
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	6	2	1	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8

Total Scores
MCC	0.495
Average MCC ± 95% Confidence Intervals	0.538 ± 0.201
Sensitivity	0.480
Positive Predictive Value	0.519
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.61	0.57	0.67	16	1425	9	0	8	1	12
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IZ4_A	tmRNA links to Rfam database...	0.31	0.31	0.33	29	25448	65	14	45	6	66
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3LA5_A	Purine links to Rfam database...	-0.02	0.00	0.00	0	938	16	0	16	0	25
3NPB_A	SAM links to Rfam database...	0.62	0.54	0.71	20	2250	10	1	7	2	17
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.59	0.45	13	4735	28	11	5	12	9
3PDR_A	ykoK links to Rfam database...	0.69	0.64	0.74	32	4797	13	3	8	2	18
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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