CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidAlifold(20)		RNAsubopt
MCC	0.695	>	0.555
Average MCC ± 95% Confidence Intervals	0.693 ± 0.065	>	0.554 ± 0.098
Sensitivity	0.540	>	0.497
Positive Predictive Value	0.897	>	0.624
Total TP	495	>	455
Total TN	191066	>	190889
Total FP	88	<	322
Total FP CONTRA	13	<	47
Total FP INCONS	44	<	227
Total FP COMP	31	<	48
Total FN	421	<	461
P-value	5.19332990918e-08

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

Total Scores
MCC	0.695
Average MCC ± 95% Confidence Intervals	0.693 ± 0.065
Sensitivity	0.540
Positive Predictive Value	0.897
Nr of predictions	23

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
3IZ4_A	tmRNA links to Rfam database...	0.58	0.39	0.88	51	70818	7	3	4	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	4	0	3	1	21
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	9	12230	9	0	7	2	24
3JYX_3	5S_rRNA links to Rfam database...	0.61	0.56	0.68	15	6306	20	0	7	13	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.70	0.54	0.89	25	6993	5	1	2	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.31	0.92	11	12391	1	0	1	0	24
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	9	2	5	2	9
3PDR_A	ykoK links to Rfam database...	0.76	0.63	0.94	45	12832	5	0	3	2	27
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
4A1C_3	5S_rRNA links to Rfam database...	0.76	0.63	0.92	34	7103	4	0	3	1	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12

Total Scores
MCC	0.555
Average MCC ± 95% Confidence Intervals	0.554 ± 0.098
Sensitivity	0.497
Positive Predictive Value	0.624
Nr of predictions	23

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	12	5	3	4	7
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
3A2K_C	tRNA links to Rfam database...	0.42	0.39	0.46	11	2902	13	2	11	0	17
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.44	0.38	0.54	15	4343	14	1	12	1	25
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3IZ4_A	tmRNA links to Rfam database...	0.51	0.47	0.56	62	70766	49	8	40	1	70
3IZF_C	5S_rRNA links to Rfam database...	0.70	0.61	0.80	33	6862	8	1	7	0	21
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2829	21	0	21	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.19	0.21	0.17	7	12204	38	11	24	3	26
3JYX_3	5S_rRNA links to Rfam database...	0.63	0.63	0.63	17	6301	21	1	9	11	10
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.75	0.65	0.86	30	6986	7	1	4	2	16
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	34	2	21	11	23
3O58_2	5S_rRNA links to Rfam database...	0.72	0.74	0.70	28	7220	13	4	8	1	10
3PDR_A	ykoK links to Rfam database...	0.75	0.63	0.90	45	12830	7	1	4	2	27
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	0	7	0	14

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