CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	PPfold(20)		RSpredict(20)
MCC	0.746	>	0.504
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.512 ± 0.298
Sensitivity	0.681	>	0.450
Positive Predictive Value	0.818	>	0.565
Total TP	1989	>	1314
Total TN	7954946	<	7955050
Total FP	607	<	1180
Total FP CONTRA	71	<	162
Total FP INCONS	371	<	851
Total FP COMP	165	<	167
Total FN	931	<	1606
P-value	0.0

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

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	0.504
Average MCC ± 95% Confidence Intervals	0.512 ± 0.298
Sensitivity	0.450
Positive Predictive Value	0.565
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...	0.71	0.62	0.81	292	1192380	91	18	50	23	176
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.36	0.34	0.38	172	1627656	314	50	232	32	330
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1674979	406	62	324	20	507
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.63	0.55	0.73	249	1119415	115	6	86	23	203
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.73	0.69	0.77	319	1135862	125	18	79	28	145
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.64	0.54	0.76	282	1204758	129	8	80	41	245

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