CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Contrafold
MCC	0.662	>	0.573
Average MCC ± 95% Confidence Intervals	0.676 ± 0.208	>	0.607 ± 0.224
Sensitivity	0.608	>	0.554
Positive Predictive Value	0.731	>	0.605
Total TP	79	>	72
Total TN	9028	>	9017
Total FP	44	<	64
Total FP CONTRA	6	<	18
Total FP INCONS	23	<	29
Total FP COMP	15	<	17
Total FN	51	<	58
P-value	0.0

Comparison of performance of ContextFold and Contrafold. 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 ContextFold and Contrafold).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Contrafold. 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 ContextFold and Contrafold).

Total Scores
MCC	0.662
Average MCC ± 95% Confidence Intervals	0.676 ± 0.208
Sensitivity	0.608
Positive Predictive Value	0.731
Nr of predictions	7

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...	0.58	0.56	0.63	10	512	6	0	6	0	8
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Total Scores
MCC	0.573
Average MCC ± 95% Confidence Intervals	0.607 ± 0.224
Sensitivity	0.554
Positive Predictive Value	0.605
Nr of predictions	7

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...	0.46	0.39	0.58	7	516	5	3	2	0	11
3J0L_a	-	0.53	0.55	0.55	6	400	6	3	2	1	5
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4AOB_A	SAM links to Rfam database...	0.53	0.52	0.56	15	1410	13	3	9	1	14
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4

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