CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Alterna		Vsfold5
MCC	0.647	>	0.568
Average MCC ± 95% Confidence Intervals	0.645 ± 0.141	>	0.578 ± 0.192
Sensitivity	0.636	>	0.537
Positive Predictive Value	0.674	>	0.621
Total TP	225	>	190
Total TN	15549	<	15577
Total FP	112	<	118
Total FP CONTRA	28	>	21
Total FP INCONS	81	<	95
Total FP COMP	3	>	2
Total FN	129	<	164
P-value	2.97012568641e-08

Comparison of performance of Alterna and Vsfold5. 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 Vsfold5).
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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for Alterna and Vsfold5. 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 Vsfold5).

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

Total Scores
MCC	0.568
Average MCC ± 95% Confidence Intervals	0.578 ± 0.192
Sensitivity	0.537
Positive Predictive Value	0.621
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.77	0.88	0.70	7	226	3	2	1	0	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.95	0.95	0.95	21	962	1	1	0	0	1
3A2K_C	tRNA links to Rfam database...	0.95	0.91	1.00	20	1088	0	0	0	0	2
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3ADB_C	-	0.72	0.61	0.87	20	1796	3	0	3	0	13
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.61	0.57	0.67	16	1425	9	0	8	1	12
3IVN_B	Purine links to Rfam database...	0.88	0.78	1.00	18	885	0	0	0	0	5
3IWN_A	c-di-GMP-I links to Rfam database...	0.26	0.25	0.30	7	1449	16	2	14	0	21
3J0L_a	-	0.39	0.36	0.44	4	402	6	4	1	1	7
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	19	4	15	0	20
3LA5_A	Purine links to Rfam database...	-0.02	0.00	0.00	0	938	16	0	16	0	25
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25

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