CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		Multilign(20)
MCC	0.712	>	0.680
Average MCC ± 95% Confidence Intervals	0.723 ± 0.195	>	0.672 ± 0.228
Sensitivity	0.684	>	0.674
Positive Predictive Value	0.749	>	0.696
Total TP	128	>	126
Total TN	12269	>	12259
Total FP	59	<	67
Total FP CONTRA	14	<	17
Total FP INCONS	29	<	38
Total FP COMP	16	>	12
Total FN	59	<	61
P-value	0.0

Comparison of performance of TurboFold(seed) and Multilign(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 TurboFold(seed) and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(seed) and Multilign(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 TurboFold(seed) and Multilign(20)).

Total Scores
MCC	0.712
Average MCC ± 95% Confidence Intervals	0.723 ± 0.195
Sensitivity	0.684
Positive Predictive Value	0.749
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.17	5	4486	37	9	16	12	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	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	0.680
Average MCC ± 95% Confidence Intervals	0.672 ± 0.228
Sensitivity	0.674
Positive Predictive Value	0.696
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

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