CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(20)		PknotsRG
MCC	0.678	>	0.598
Average MCC ± 95% Confidence Intervals	0.666 ± 0.105	>	0.601 ± 0.137
Sensitivity	0.640	>	0.633
Positive Predictive Value	0.724	>	0.571
Total TP	372	>	368
Total TN	68015	>	67884
Total FP	216	<	358
Total FP CONTRA	69	<	93
Total FP INCONS	73	<	184
Total FP COMP	74	<	81
Total FN	209	<	213
P-value	5.19332990918e-08

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

Total Scores
MCC	0.678
Average MCC ± 95% Confidence Intervals	0.666 ± 0.105
Sensitivity	0.640
Positive Predictive Value	0.724
Nr of predictions	21

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
3J20_0	tRNA links to Rfam database...	0.93	0.90	0.95	19	1199	1	1	0	0	2
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.21	0.20	0.23	3	2729	15	4	6	5	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.53	0.43	10	4738	29	7	6	16	9
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.41	9	5352	15	3	10	2	20
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.65	0.58	0.74	14	1183	6	2	3	1	10

Total Scores
MCC	0.598
Average MCC ± 95% Confidence Intervals	0.601 ± 0.137
Sensitivity	0.633
Positive Predictive Value	0.571
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3GX2_A	SAM links to Rfam database...	0.80	0.79	0.81	22	1422	6	2	3	1	6
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...	0.56	0.60	0.52	57	25426	57	25	28	4	38
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	30	6	13	11	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.32	0.42	0.24	8	4728	40	12	13	15	11
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1089	22	4	18	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...	0.93	0.86	1.00	32	2246	4	0	0	4	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3PDR_A	ykoK links to Rfam database...	0.90	0.90	0.90	45	4790	7	2	3	2	5
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	44	5	23	16	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	43	11	20	12	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15

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