CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	ContextFold		PPfold(20)
MCC	0.753	>	0.746
Average MCC ± 95% Confidence Intervals	0.759 ± 0.199	>	0.747 ± 0.127
Sensitivity	0.710	>	0.681
Positive Predictive Value	0.799	<	0.818
Total TP	2073	>	1989
Total TN	7954783	<	7954946
Total FP	619	>	607
Total FP CONTRA	98	>	71
Total FP INCONS	423	>	371
Total FP COMP	98	<	165
Total FN	847	<	931
P-value	0.0

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

Total Scores
MCC	0.753
Average MCC ± 95% Confidence Intervals	0.759 ± 0.199
Sensitivity	0.710
Positive Predictive Value	0.799
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...	0.86	0.80	0.91	376	1192327	51	4	33	14	92
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.58	0.54	0.63	271	1627677	194	30	132	32	231
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.46	0.45	0.47	227	1674887	268	53	198	17	280
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.85	0.79	0.91	358	1119364	45	3	31	11	94
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.92	0.90	0.95	419	1135835	28	6	18	4	45
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.88	0.80	0.97	422	1204693	33	2	11	20	105

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

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