CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		RNASampler(seed)
MCC	0.659	>	0.601
Average MCC ± 95% Confidence Intervals	0.699 ± 0.193	>	0.587 ± 0.230
Sensitivity	0.579	>	0.433
Positive Predictive Value	0.755	<	0.839
Total TP	139	>	104
Total TN	29854	<	29914
Total FP	55	>	25
Total FP CONTRA	5	>	2
Total FP INCONS	40	>	18
Total FP COMP	10	>	5
Total FN	101	<	136
P-value	0.0

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

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.699 ± 0.193
Sensitivity	0.579
Positive Predictive Value	0.755
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.92	0.84	1.00	21	2124	0	0	0	0	4
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.83	1.00	20	2060	0	0	0	0	4
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.52	15	4724	15	0	14	1	25

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.587 ± 0.230
Sensitivity	0.433
Positive Predictive Value	0.839
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.82	0.68	1.00	17	2128	0	0	0	0	8
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.67	1.00	16	2064	0	0	0	0	8
2L94_A	HIV_FE links to Rfam database...	0.71	0.55	0.92	11	978	1	0	1	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.30	1.00	12	4741	1	0	0	1	28

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