CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Contrafold
MCC	0.746	>	0.470
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.472 ± 0.096
Sensitivity	0.681	>	0.453
Positive Predictive Value	0.818	>	0.489
Total TP	1989	>	1323
Total TN	7954946	>	7954670
Total FP	607	<	1590
Total FP CONTRA	71	<	215
Total FP INCONS	371	<	1169
Total FP COMP	165	<	206
Total FN	931	<	1597
P-value	0.0

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

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	0.470
Average MCC ± 95% Confidence Intervals	0.472 ± 0.096
Sensitivity	0.453
Positive Predictive Value	0.489
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...	0.47	0.44	0.50	206	1192327	232	26	181	25	262
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.50	0.49	0.51	246	1627630	284	52	182	50	256
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.39	0.40	0.38	202	1674827	390	57	279	54	305
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.36	0.35	0.38	157	1119345	281	41	213	27	295
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.62	0.60	0.64	280	1135838	187	19	141	27	184
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.49	0.44	0.55	232	1204703	216	20	173	23	295

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