CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		RDfolder
MCC	0.829	>	0.608
Average MCC ± 95% Confidence Intervals	0.807 ± 0.113	>	0.603 ± 0.206
Sensitivity	0.770	>	0.533
Positive Predictive Value	0.900	>	0.711
Total TP	117	>	81
Total TN	6861	<	6877
Total FP	15	<	35
Total FP CONTRA	6	<	8
Total FP INCONS	7	<	25
Total FP COMP	2	=	2
Total FN	35	<	71
P-value	0.0

Comparison of performance of PPfold(20) and RDfolder. 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 PPfold(20) and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and RDfolder. 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 PPfold(20) and RDfolder).

Total Scores
MCC	0.829
Average MCC ± 95% Confidence Intervals	0.807 ± 0.113
Sensitivity	0.770
Positive Predictive Value	0.900
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J3D_C	tRNA links to Rfam database...	0.87	0.89	0.85	17	948	3	3	0	0	2
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7

Total Scores
MCC	0.608
Average MCC ± 95% Confidence Intervals	0.603 ± 0.206
Sensitivity	0.533
Positive Predictive Value	0.711
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.82	0.76	0.89	16	1201	3	1	1	1	5
3J3D_C	tRNA links to Rfam database...	0.76	0.79	0.75	15	948	5	3	2	0	4
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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