CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		RDfolder
MCC	0.771	>	0.456
Average MCC ± 95% Confidence Intervals	0.734 ± 0.180	>	0.459 ± 0.265
Sensitivity	0.713	>	0.420
Positive Predictive Value	0.843	>	0.516
Total TP	107	>	63
Total TN	6982	<	6987
Total FP	31	<	61
Total FP CONTRA	7	<	12
Total FP INCONS	13	<	47
Total FP COMP	11	>	2
Total FN	43	<	87
P-value	0.0

Comparison of performance of PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and RDfolder).

Total Scores
MCC	0.771
Average MCC ± 95% Confidence Intervals	0.734 ± 0.180
Sensitivity	0.713
Positive Predictive Value	0.843
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.41	0.33	0.55	6	517	5	0	5	0	12
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	4	3	0	1	1
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.73	0.89	24	1962	6	1	2	3	9
4AOB_A	SAM links to Rfam database...	0.85	0.79	0.92	23	1412	4	0	2	2	6
4ENB_A	crcB links to Rfam database...	0.61	0.53	0.73	8	461	5	1	2	2	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	5	1	2	2	7

Total Scores
MCC	0.456
Average MCC ± 95% Confidence Intervals	0.459 ± 0.265
Sensitivity	0.420
Positive Predictive Value	0.516
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	514	14	3	11	0	18
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
3W3S_B	tRNA-Sec links to Rfam database...	0.29	0.27	0.33	9	1962	18	2	16	0	24
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.