CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(seed)		Afold
MCC	0.588	>	0.400
Average MCC ± 95% Confidence Intervals	0.472 ± 0.117	>	0.439 ± 0.155
Sensitivity	0.501	>	0.390
Positive Predictive Value	0.692	>	0.412
Total TP	344	>	268
Total TN	1012223	>	1012069
Total FP	175	<	417
Total FP CONTRA	6	<	54
Total FP INCONS	147	<	329
Total FP COMP	22	<	34
Total FN	343	<	419
P-value	1.70887622364e-08

Comparison of performance of Murlet(seed) and Afold. 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 Murlet(seed) and Afold).
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 Murlet(seed) and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(seed) and Afold. 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 Murlet(seed) and Afold).

Total Scores
MCC	0.588
Average MCC ± 95% Confidence Intervals	0.472 ± 0.117
Sensitivity	0.501
Positive Predictive Value	0.692
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.64	0.61	0.68	263	977515	145	6	117	22	171
PDB_00716	HDV_ribozyme links to Rfam database...	0.23	0.13	0.43	3	2694	4	0	4	0	20
PDB_01092	glmS links to Rfam database...	0.69	0.48	1.00	25	10128	0	0	0	0	27
RFA_00632	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	4088	4	0	4	0	25
RFA_00636	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	3998	4	0	4	0	25
RFA_00767	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1882	3	0	3	0	12
RFA_00768	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1883	3	0	3	0	13
RFA_00769	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	1942	3	0	3	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	2005	3	0	3	0	10
RFA_00773	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1945	3	0	3	0	13
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.50	0.38	0.67	6	2136	3	0	3	0	10

Total Scores
MCC	0.400
Average MCC ± 95% Confidence Intervals	0.439 ± 0.155
Sensitivity	0.390
Positive Predictive Value	0.412
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.37	0.37	0.37	160	977470	284	42	229	13	274
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2677	25	1	23	1	23
PDB_01092	glmS links to Rfam database...	0.69	0.60	0.79	31	10114	11	1	7	3	21
RFA_00632	HDV_ribozyme links to Rfam database...	0.40	0.39	0.41	11	4068	18	0	16	2	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	17	2	14	1	16
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	5	0	4	1	8
RFA_00768	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	8	1	6	1	10
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	10	3	5	2	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	6	0	2	4	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	5	1	0	4	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	16	2	13	1	16
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	12	1	10	1	10

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