CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RNAsubopt
MCC	0.662	>	0.402
Average MCC ± 95% Confidence Intervals	0.676 ± 0.208	>	0.404 ± 0.267
Sensitivity	0.608	>	0.423
Positive Predictive Value	0.731	>	0.399
Total TP	79	>	55
Total TN	9028	>	8998
Total FP	44	<	100
Total FP CONTRA	6	<	26
Total FP INCONS	23	<	57
Total FP COMP	15	<	17
Total FN	51	<	75
P-value	0.0

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

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	0.402
Average MCC ± 95% Confidence Intervals	0.404 ± 0.267
Sensitivity	0.423
Positive Predictive Value	0.399
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	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	7	0	7	0	10

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