CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		Fold
MCC	0.530	>	0.496
Average MCC ± 95% Confidence Intervals	0.597 ± 0.167	>	0.480 ± 0.198
Sensitivity	0.590	>	0.539
Positive Predictive Value	0.482	>	0.462
Total TP	210	>	192
Total TN	64794	<	64814
Total FP	283	=	283
Total FP CONTRA	94	>	85
Total FP INCONS	132	<	139
Total FP COMP	57	<	59
Total FN	146	<	164
P-value	2.12160100812e-08

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

Total Scores
MCC	0.530
Average MCC ± 95% Confidence Intervals	0.597 ± 0.167
Sensitivity	0.590
Positive Predictive Value	0.482
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

Total Scores
MCC	0.496
Average MCC ± 95% Confidence Intervals	0.480 ± 0.198
Sensitivity	0.539
Positive Predictive Value	0.462
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3IYQ_A	tmRNA links to Rfam database...	0.24	0.33	0.18	17	22345	95	40	38	17	34
3IZ4_A	tmRNA links to Rfam database...	0.60	0.61	0.59	58	25437	47	16	25	6	37
3NKB_B	-	0.41	0.42	0.42	8	716	11	4	7	0	11
3NPB_A	SAM links to Rfam database...	0.77	0.73	0.82	27	2245	11	0	6	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.50	0.31	11	4728	41	9	16	16	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10

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