CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		RSpredict(20)
MCC	0.595	>	0.484
Average MCC ± 95% Confidence Intervals	0.626 ± 0.187	>	0.484 ± 0.159
Sensitivity	0.490	>	0.373
Positive Predictive Value	0.729	>	0.636
Total TP	129	>	98
Total TN	32833	<	32856
Total FP	58	<	62
Total FP CONTRA	6	<	7
Total FP INCONS	42	<	49
Total FP COMP	10	>	6
Total FN	134	<	165
P-value	0.0

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

Total Scores
MCC	0.595
Average MCC ± 95% Confidence Intervals	0.626 ± 0.187
Sensitivity	0.490
Positive Predictive Value	0.729
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...	0.92	0.90	0.95	18	971	1	0	1	0	2
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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.484
Average MCC ± 95% Confidence Intervals	0.484 ± 0.159
Sensitivity	0.373
Positive Predictive Value	0.636
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...	0.55	0.50	0.63	10	974	6	0	6	0	10
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.18	0.20	6	11751	30	6	18	6	27
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.33	0.69	18	7114	8	0	8	0	36
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.