CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		IPknot
MCC	0.621	>	0.536
Average MCC ± 95% Confidence Intervals	0.620 ± 0.161	>	0.537 ± 0.095
Sensitivity	0.544	>	0.466
Positive Predictive Value	0.708	>	0.616
Total TP	2368	>	2026
Total TN	12465477	<	12465534
Total FP	1159	<	1493
Total FP CONTRA	149	<	180
Total FP INCONS	828	<	1082
Total FP COMP	182	<	231
Total FN	1981	<	2323
P-value	0.0

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

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	0.536
Average MCC ± 95% Confidence Intervals	0.537 ± 0.095
Sensitivity	0.466
Positive Predictive Value	0.616
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...	0.59	0.53	0.65	252	1178495	145	17	116	12	221
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.57	0.52	0.63	250	1198526	164	23	127	14	228
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.60	0.48	0.74	218	1129962	95	5	71	19	232
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.67	0.58	0.77	265	1117916	90	11	68	11	188
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.35	0.31	0.39	160	1988600	320	42	213	65	357
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.40	0.34	0.46	170	1615137	238	31	165	42	326
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.41	0.33	0.51	163	1665906	188	30	126	32	332
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.55	0.46	0.66	206	1137473	121	11	96	14	241
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.69	0.63	0.76	342	1433519	132	10	100	22	198

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