CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		UNAFold
MCC	0.746	>	0.441
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.443 ± 0.102
Sensitivity	0.681	>	0.430
Positive Predictive Value	0.818	>	0.452
Total TP	1989	>	1257
Total TN	7954946	>	7954594
Total FP	607	<	1701
Total FP CONTRA	71	<	248
Total FP INCONS	371	<	1278
Total FP COMP	165	<	175
Total FN	931	<	1663
P-value	0.0

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

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	0.441
Average MCC ± 95% Confidence Intervals	0.443 ± 0.102
Sensitivity	0.430
Positive Predictive Value	0.452
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...	0.50	0.49	0.52	228	1192304	228	35	173	20	240
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.35	0.35	0.35	176	1627600	377	65	269	43	326
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.39	0.39	0.39	200	1674848	370	67	250	53	307
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.35	0.34	0.37	153	1119337	287	30	236	21	299
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.59	0.58	0.61	268	1135838	197	24	148	25	196
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.47	0.44	0.50	232	1204667	242	27	202	13	295

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