CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	McQFold		TurboFold(20)
MCC	0.685	>	0.653
Average MCC ± 95% Confidence Intervals	0.733 ± 0.336	>	0.668 ± 0.244
Sensitivity	0.705	>	0.606
Positive Predictive Value	0.674	<	0.714
Total TP	93	>	80
Total TN	9182	<	9208
Total FP	52	>	42
Total FP CONTRA	16	>	11
Total FP INCONS	29	>	21
Total FP COMP	7	<	10
Total FN	39	<	52
P-value	0.0

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

Total Scores
MCC	0.685
Average MCC ± 95% Confidence Intervals	0.733 ± 0.336
Sensitivity	0.705
Positive Predictive Value	0.674
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.82	0.83	0.83	24	1504	5	1	4	0	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

Total Scores
MCC	0.653
Average MCC ± 95% Confidence Intervals	0.668 ± 0.244
Sensitivity	0.606
Positive Predictive Value	0.714
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.22	0.25	0.21	5	4492	28	6	13	9	15
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

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