CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Carnac(20)
MCC	0.746	>	0.564
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.561 ± 0.077
Sensitivity	0.681	>	0.338
Positive Predictive Value	0.818	<	0.940
Total TP	1989	>	987
Total TN	7954946	<	7956327
Total FP	607	>	136
Total FP CONTRA	71	>	12
Total FP INCONS	371	>	51
Total FP COMP	165	>	73
Total FN	931	<	1933
P-value	0.0

Comparison of performance of PPfold(20) and Carnac(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 Carnac(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 Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and Carnac(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 Carnac(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	0.564
Average MCC ± 95% Confidence Intervals	0.561 ± 0.077
Sensitivity	0.338
Positive Predictive Value	0.940
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...	0.64	0.43	0.97	200	1192533	11	3	4	4	268
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.45	0.23	0.92	113	1627987	32	1	9	22	389
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.49	0.25	0.96	129	1675231	29	0	5	24	378
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.55	0.33	0.93	148	1119597	15	1	10	4	304
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.60	0.39	0.93	181	1136084	19	3	10	6	283
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.62	0.41	0.93	216	1204895	30	4	13	13	311

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