CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(seed)		CentroidFold
MCC	0.584	>	0.528
Average MCC ± 95% Confidence Intervals	0.476 ± 0.098	<	0.623 ± 0.088
Sensitivity	0.492	>	0.465
Positive Predictive Value	0.694	>	0.602
Total TP	354	>	334
Total TN	1015109	>	1015064
Total FP	180	<	240
Total FP CONTRA	6	<	34
Total FP INCONS	150	<	187
Total FP COMP	24	>	19
Total FN	365	<	385
P-value	2.89431173416e-06

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

Total Scores
MCC	0.584
Average MCC ± 95% Confidence Intervals	0.476 ± 0.098
Sensitivity	0.492
Positive Predictive Value	0.694
Nr of predictions	14

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_00005	Tymo_tRNA-like links to Rfam database...	0.53	0.29	1.00	4	942	2	0	0	2	10
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_00779	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1944	3	0	3	0	12
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	0.528
Average MCC ± 95% Confidence Intervals	0.623 ± 0.088
Sensitivity	0.465
Positive Predictive Value	0.602
Nr of predictions	14

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...	0.46	0.41	0.52	176	977564	173	23	138	12	258
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00716	HDV_ribozyme links to Rfam database...	0.33	0.30	0.37	7	2682	13	0	12	1	16
PDB_01092	glmS links to Rfam database...	0.71	0.63	0.80	33	10112	10	1	7	2	19
RFA_00632	HDV_ribozyme links to Rfam database...	0.67	0.61	0.74	17	4072	6	1	5	0	11
RFA_00636	HDV_ribozyme links to Rfam database...	0.64	0.64	0.64	18	3977	10	4	6	0	10
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.45	0.44	0.47	8	1874	9	1	8	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.64	0.50	0.82	9	2005	4	0	2	2	9
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	3	1	0	2	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	0	2	0	8
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...	0.43	0.38	0.50	6	2133	6	0	6	0	10

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