CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		MXScarna(20)
MCC	0.746	>	0.629
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.633 ± 0.123
Sensitivity	0.681	>	0.574
Positive Predictive Value	0.818	>	0.689
Total TP	1989	>	1677
Total TN	7954946	>	7954943
Total FP	607	<	1042
Total FP CONTRA	71	<	118
Total FP INCONS	371	<	639
Total FP COMP	165	<	285
Total FN	931	<	1243
P-value	0.0

Comparison of performance of PPfold(20) and MXScarna(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 MXScarna(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 MXScarna(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and MXScarna(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 MXScarna(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	0.629
Average MCC ± 95% Confidence Intervals	0.633 ± 0.123
Sensitivity	0.574
Positive Predictive Value	0.689
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...	0.70	0.64	0.77	299	1192353	124	11	77	36	169
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.49	0.45	0.53	227	1627679	267	35	169	63	275
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.48	0.44	0.53	224	1674941	262	38	162	62	283
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.72	0.67	0.78	303	1119366	134	11	76	47	149
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.74	0.69	0.79	322	1135872	121	12	72	37	142
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.66	0.57	0.76	302	1204732	134	11	83	40	225

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