CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		RNAfold
MCC	0.746	>	0.424
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.425 ± 0.110
Sensitivity	0.681	>	0.420
Positive Predictive Value	0.818	>	0.428
Total TP	1989	>	1227
Total TN	7954946	>	7954512
Total FP	607	<	1810
Total FP CONTRA	71	<	268
Total FP INCONS	371	<	1370
Total FP COMP	165	<	172
Total FN	931	<	1693
P-value	0.0

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

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	0.424
Average MCC ± 95% Confidence Intervals	0.425 ± 0.110
Sensitivity	0.420
Positive Predictive Value	0.428
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...	0.41	0.41	0.42	190	1192286	279	40	224	15	278
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.38	0.38	0.37	190	1627600	364	68	252	44	312
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.39	0.39	0.38	199	1674839	381	67	260	54	308
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.31	0.31	0.31	138	1119315	322	37	266	19	314
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.62	0.61	0.62	282	1135826	195	25	145	25	182
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.45	0.43	0.47	228	1204646	269	31	223	15	299

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