CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		RSpredict(20)
MCC	0.661	>	0.618
Average MCC ± 95% Confidence Intervals	0.682 ± 0.122	>	0.604 ± 0.132
Sensitivity	0.553	>	0.501
Positive Predictive Value	0.796	>	0.768
Total TP	226	>	205
Total TN	58114	<	58131
Total FP	73	>	65
Total FP CONTRA	11	<	17
Total FP INCONS	47	>	45
Total FP COMP	15	>	3
Total FN	183	<	204
P-value	1.00475527001e-08

Comparison of performance of Cylofold and RSpredict(20). 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 RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and RSpredict(20). 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 RSpredict(20)).

Total Scores
MCC	0.661
Average MCC ± 95% Confidence Intervals	0.682 ± 0.122
Sensitivity	0.553
Positive Predictive Value	0.796
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3PDR_A	ykoK links to Rfam database...	0.72	0.54	0.95	39	12839	4	0	2	2	33
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
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Total Scores
MCC	0.618
Average MCC ± 95% Confidence Intervals	0.604 ± 0.132
Sensitivity	0.501
Positive Predictive Value	0.768
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3AMU_B	tRNA links to Rfam database...	0.61	0.41	0.92	11	2991	1	0	1	0	16
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	3	1	2	0	21
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.34	0.30	12	12363	28	12	16	0	23
3PDR_A	ykoK links to Rfam database...	0.67	0.49	0.92	35	12842	5	0	3	2	37
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.68	0.60	0.78	25	3884	7	1	6	0	17
4AOB_A	SAM links to Rfam database...	0.28	0.14	0.55	6	4360	5	0	5	0	36
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.45	0.32	0.67	6	1317	3	0	3	0	13

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