CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		CentroidFold
MCC	0.621	>	0.486
Average MCC ± 95% Confidence Intervals	0.620 ± 0.161	>	0.486 ± 0.073
Sensitivity	0.544	>	0.413
Positive Predictive Value	0.708	>	0.572
Total TP	2368	>	1798
Total TN	12465477	<	12465679
Total FP	1159	<	1618
Total FP CONTRA	149	<	166
Total FP INCONS	828	<	1179
Total FP COMP	182	<	273
Total FN	1981	<	2551
P-value	0.0

Comparison of performance of Murlet(20) 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(20) 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(20) and CentroidFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) 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(20) and CentroidFold).

Total Scores
MCC	0.621
Average MCC ± 95% Confidence Intervals	0.620 ± 0.161
Sensitivity	0.544
Positive Predictive Value	0.708
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.75	0.70	0.81	330	1178473	93	14	63	16	143
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.75	0.68	0.84	325	1198537	73	14	50	9	153
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.75	0.67	0.83	302	1129893	75	12	49	14	148
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.78	0.72	0.85	328	1117874	75	11	47	17	125
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.39	0.31	0.49	160	1988690	189	26	139	24	357
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.31	0.25	0.40	122	1615195	206	23	163	20	374
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.33	0.29	0.36	146	1665818	288	38	223	27	349
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.78	0.71	0.86	318	1137416	79	8	44	27	129
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.73	0.62	0.86	337	1433581	81	3	50	28	203

Total Scores
MCC	0.486
Average MCC ± 95% Confidence Intervals	0.486 ± 0.073
Sensitivity	0.413
Positive Predictive Value	0.572
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.52	0.45	0.59	213	1178522	162	17	128	17	260
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.57	0.50	0.66	237	1198568	130	20	101	9	241
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.49	0.41	0.57	186	1129931	157	13	126	18	264
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.53	0.42	0.67	192	1117973	105	9	86	10	261
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.30	0.25	0.36	131	1988654	302	33	197	72	386
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.42	0.35	0.49	173	1615153	226	27	150	49	323
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.42	0.36	0.48	180	1665851	239	34	160	45	315
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.51	0.40	0.65	179	1137510	120	5	92	23	268
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.62	0.57	0.68	307	1433517	177	8	139	30	233

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