CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Fold
MCC	0.746	>	0.375
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.376 ± 0.040
Sensitivity	0.681	>	0.375
Positive Predictive Value	0.818	>	0.375
Total TP	1989	>	1096
Total TN	7954946	>	7954456
Total FP	607	<	1989
Total FP CONTRA	71	<	288
Total FP INCONS	371	<	1537
Total FP COMP	165	>	164
Total FN	931	<	1824
P-value	0.0

Comparison of performance of PPfold(20) and Fold. 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 Fold).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for PPfold(20) and Fold).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and Fold. 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 Fold).

Total Scores
MCC	0.746
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127
Sensitivity	0.681
Positive Predictive Value	0.818
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.87	363	1192324	70	13	40	17	105
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.64	0.56	0.73	280	1627728	143	17	85	41	222
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.56	0.49	0.64	246	1674980	178	15	124	39	261
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.90	367	1119348	69	4	37	28	85
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.86	374	1135845	75	15	44	16	90
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.78	0.68	0.88	359	1204721	72	7	41	24	168

Total Scores
MCC	0.375
Average MCC ± 95% Confidence Intervals	0.376 ± 0.040
Sensitivity	0.375
Positive Predictive Value	0.375
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.39	0.39	0.40	183	1192281	294	41	235	18	285
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.40	0.40	0.39	203	1627589	370	67	251	52	299
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.36	0.37	0.35	186	1674831	392	68	280	44	321
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.42	0.42	0.42	191	1119306	279	34	225	20	261
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.37	0.38	0.37	175	1135806	315	41	256	18	289
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.31	0.30	0.33	158	1204643	339	37	290	12	369

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