CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Sfold
MCC	0.746	>	0.480
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.486 ± 0.103
Sensitivity	0.681	>	0.397
Positive Predictive Value	0.818	>	0.580
Total TP	1989	>	1158
Total TN	7954946	<	7955382
Total FP	607	<	952
Total FP CONTRA	71	<	147
Total FP INCONS	371	<	690
Total FP COMP	165	>	115
Total FN	931	<	1762
P-value	0.0

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

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	0.480
Average MCC ± 95% Confidence Intervals	0.486 ± 0.103
Sensitivity	0.397
Positive Predictive Value	0.580
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...	0.37	0.33	0.42	155	1192370	232	35	180	17	313
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.46	0.37	0.56	187	1627778	175	32	113	30	315
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.38	0.33	0.43	166	1674980	241	44	175	22	341
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.58	0.40	0.84	179	1119542	50	5	30	15	273
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.59	0.52	0.66	241	1135913	144	19	105	20	223
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.55	0.44	0.70	230	1204799	110	12	87	11	297

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