CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Fold
MCC	0.662	>	0.348
Average MCC ± 95% Confidence Intervals	0.676 ± 0.208	>	0.317 ± 0.214
Sensitivity	0.608	>	0.362
Positive Predictive Value	0.731	>	0.353
Total TP	79	>	47
Total TN	9028	>	9003
Total FP	44	<	104
Total FP CONTRA	6	<	24
Total FP INCONS	23	<	62
Total FP COMP	15	<	18
Total FN	51	<	83
P-value	0.0

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

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	0.348
Average MCC ± 95% Confidence Intervals	0.317 ± 0.214
Sensitivity	0.362
Positive Predictive Value	0.353
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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J0L_a	-	0.15	0.18	0.17	2	399	11	4	6	1	9
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
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

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