CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Cylofold
MCC	0.683	>	0.603
Average MCC ± 95% Confidence Intervals	0.621 ± 0.215	<	0.628 ± 0.180
Sensitivity	0.638	>	0.583
Positive Predictive Value	0.743	>	0.640
Total TP	150	>	137
Total TN	11440	>	11428
Total FP	56	<	81
Total FP CONTRA	16	<	25
Total FP INCONS	36	<	52
Total FP COMP	4	=	4
Total FN	85	<	98
P-value	1.66062906821e-08

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

Total Scores
MCC	0.683
Average MCC ± 95% Confidence Intervals	0.621 ± 0.215
Sensitivity	0.638
Positive Predictive Value	0.743
Nr of predictions	12

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
2M58_A	-	-0.02	0.00	0.00	0	530	14	3	11	0	12
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.85	0.90	28	1958	4	0	3	1	5
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ATO_G	-	-0.02	0.00	0.00	0	218	2	1	1	0	7
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.42	0.39	0.46	11	1824	13	6	7	0	17

Total Scores
MCC	0.603
Average MCC ± 95% Confidence Intervals	0.628 ± 0.180
Sensitivity	0.583
Positive Predictive Value	0.640
Nr of predictions	12

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	5	1	4	0	7
2M58_A	-	0.60	0.58	0.64	7	533	4	1	3	0	5
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3
4FRN_A	AdoCbl-variant links to Rfam database...	0.23	0.18	0.31	5	1832	11	7	4	0	23

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