CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		NanoFolder
MCC	0.520	>	0.410
Average MCC ± 95% Confidence Intervals	0.557 ± 0.177	>	0.433 ± 0.119
Sensitivity	0.433	>	0.411
Positive Predictive Value	0.634	>	0.420
Total TP	97	>	92
Total TN	22694	>	22628
Total FP	57	<	129
Total FP CONTRA	5	<	16
Total FP INCONS	51	<	111
Total FP COMP	1	<	2
Total FN	127	<	132
P-value	0.0

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

Total Scores
MCC	0.520
Average MCC ± 95% Confidence Intervals	0.557 ± 0.177
Sensitivity	0.433
Positive Predictive Value	0.634
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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Total Scores
MCC	0.410
Average MCC ± 95% Confidence Intervals	0.433 ± 0.119
Sensitivity	0.411
Positive Predictive Value	0.420
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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

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