CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		MCFold
MCC	0.649	>	0.521
Average MCC ± 95% Confidence Intervals	0.646 ± 0.151	>	0.491 ± 0.144
Sensitivity	0.636	>	0.548
Positive Predictive Value	0.678	>	0.516
Total TP	204	>	176
Total TN	13763	>	13723
Total FP	100	<	176
Total FP CONTRA	27	<	36
Total FP INCONS	70	<	129
Total FP COMP	3	<	11
Total FN	117	<	145
P-value	2.78993384543e-08

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

Total Scores
MCC	0.649
Average MCC ± 95% Confidence Intervals	0.646 ± 0.151
Sensitivity	0.636
Positive Predictive Value	0.678
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.44	0.53	8	513	7	0	7	0	10
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.56	0.57	0.57	16	1421	13	4	8	1	12
3IVN_B	Purine links to Rfam database...	0.81	0.78	0.86	18	882	3	2	1	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.81	0.79	0.85	22	1446	5	1	3	1	6
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
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
3NKB_B	-	0.41	0.42	0.42	8	716	11	3	8	0	11
3RKF_A	Purine links to Rfam database...	0.82	0.79	0.86	19	844	3	1	2	0	5
3SD1_A	THF links to Rfam database...	0.55	0.55	0.57	16	1505	12	4	8	0	13

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.491 ± 0.144
Sensitivity	0.548
Positive Predictive Value	0.516
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.54	0.63	0.50	5	226	5	2	3	0	3
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
2RP0_A	-	0.70	0.71	0.71	5	109	2	1	1	0	2
2ZZN_D	tRNA links to Rfam database...	0.69	0.73	0.67	16	960	11	1	7	3	6
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3GCA_A	-	-0.05	0.00	0.00	0	150	8	4	4	0	7
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.19	0.21	0.20	6	1442	24	5	19	0	22
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3JYV_7	tRNA links to Rfam database...	0.25	0.30	0.24	6	1086	20	8	11	1	14
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3NKB_B	-	0.68	0.74	0.64	14	713	8	2	6	0	5
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16

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