CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	RNAfold		Alterna
MCC	0.668	>	0.647
Average MCC ± 95% Confidence Intervals	0.638 ± 0.170	<	0.645 ± 0.141
Sensitivity	0.655	>	0.636
Positive Predictive Value	0.695	>	0.674
Total TP	232	>	225
Total TN	15549	=	15549
Total FP	107	<	112
Total FP CONTRA	21	<	28
Total FP INCONS	81	=	81
Total FP COMP	5	>	3
Total FN	122	<	129
P-value	3.10499527239e-08

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

Total Scores
MCC	0.668
Average MCC ± 95% Confidence Intervals	0.638 ± 0.170
Sensitivity	0.655
Positive Predictive Value	0.695
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
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	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.35	0.36	0.36	12	1786	22	1	20	1	21
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.81	0.79	0.85	22	1423	5	2	2	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.69	0.68	0.70	19	1445	9	1	7	1	9
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	-	0.69	0.74	0.67	14	714	7	0	7	0	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...	0.77	0.76	0.79	22	1505	6	4	2	0	7

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.645 ± 0.141
Sensitivity	0.636
Positive Predictive Value	0.674
Nr of predictions	17

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
3ADB_C	-	0.63	0.64	0.64	21	1786	12	1	11	0	12
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

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