CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		Alterna
MCC	0.546	>	0.518
Average MCC ± 95% Confidence Intervals	0.520 ± 0.131	<	0.520 ± 0.118
Sensitivity	0.475	>	0.447
Positive Predictive Value	0.637	>	0.612
Total TP	304	>	286
Total TN	54153	<	54163
Total FP	180	<	188
Total FP CONTRA	13	<	18
Total FP INCONS	160	<	163
Total FP COMP	7	=	7
Total FN	336	<	354
P-value	5.50294594097e-08

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

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.520 ± 0.131
Sensitivity	0.475
Positive Predictive Value	0.637
Nr of predictions	25

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KFC_A	-	-0.02	0.00	0.00	0	622	8	0	8	0	20
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2RP0_A	-	0.58	0.42	0.83	5	345	1	0	1	0	7
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_D	-	0.18	0.15	0.24	4	1936	13	0	13	0	22
2WW9_E	-	0.47	0.29	0.80	4	556	1	0	1	0	10
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.25	6	3462	18	0	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.80	0.74	0.87	20	2462	3	0	3	0	7
3A2K_C	tRNA links to Rfam database...	0.41	0.39	0.44	11	2901	14	2	12	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.70	1.00	26	3629	0	0	0	0	11
3ADB_C	-	0.78	0.74	0.82	28	4152	6	0	6	0	10
3AKZ_H	tRNA links to Rfam database...	0.16	0.14	0.19	4	2680	17	2	15	0	24
3AM1_B	-	0.72	0.66	0.79	23	3211	6	0	6	0	12
3GCA_A	-	-0.02	0.00	0.00	0	519	9	0	9	0	17
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.62	0.58	0.68	19	4250	9	0	9	0	14
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2827	23	1	22	0	32
3KTW_C	-	0.71	0.63	0.82	27	4527	7	2	4	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14

Total Scores
MCC	0.518
Average MCC ± 95% Confidence Intervals	0.520 ± 0.118
Sensitivity	0.447
Positive Predictive Value	0.612
Nr of predictions	25

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KFC_A	-	0.49	0.25	1.00	5	625	0	0	0	0	15
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_D	-	-0.01	0.00	0.00	0	1936	17	1	16	0	26
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WW9_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2ZZM_B	tRNA links to Rfam database...	0.10	0.09	0.13	3	3463	20	2	18	0	29
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.70	1.00	26	3629	0	0	0	0	11
3ADB_C	-	0.59	0.55	0.64	21	4153	12	0	12	0	17
3AKZ_H	tRNA links to Rfam database...	0.40	0.39	0.42	11	2675	15	4	11	0	17
3AM1_B	-	0.61	0.57	0.67	20	3210	10	1	9	0	15
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3IVN_B	Purine links to Rfam database...	0.74	0.61	0.90	19	2325	2	1	1	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.75	0.67	0.85	22	4252	5	0	4	1	11
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2828	22	0	22	0	32
3KTW_C	-	0.39	0.35	0.45	15	4527	19	1	17	1	28
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NKB_B	-	0.35	0.31	0.42	8	1997	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15

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