CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		Contrafold
MCC	0.621	>	0.467
Average MCC ± 95% Confidence Intervals	0.620 ± 0.161	>	0.469 ± 0.074
Sensitivity	0.544	>	0.447
Positive Predictive Value	0.708	>	0.488
Total TP	2368	>	1944
Total TN	12465477	>	12464842
Total FP	1159	<	2385
Total FP CONTRA	149	<	268
Total FP INCONS	828	<	1768
Total FP COMP	182	<	349
Total FN	1981	<	2405
P-value	0.0

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

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	0.467
Average MCC ± 95% Confidence Intervals	0.469 ± 0.074
Sensitivity	0.447
Positive Predictive Value	0.488
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...	0.50	0.48	0.52	228	1178444	227	20	188	19	245
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.61	267	1198490	184	24	145	15	211
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.44	0.42	0.47	190	1129849	240	28	189	23	260
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.55	0.51	0.60	232	1117873	173	15	140	18	221
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.33	0.32	0.33	166	1988512	422	56	281	85	351
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.39	0.36	0.42	181	1615070	306	41	211	54	315
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.36	0.37	0.36	181	1665721	382	54	269	59	314
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.48	0.44	0.53	196	1137416	209	14	160	35	251
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.58	0.56	0.60	303	1433467	242	16	185	41	237

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