CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		RSpredict(20)
MCC	0.621	>	0.013
Average MCC ± 95% Confidence Intervals	0.620 ± 0.161	>	0.014 ± 0.011
Sensitivity	0.544	>	0.013
Positive Predictive Value	0.708	>	0.015
Total TP	2368	>	55
Total TN	12465477	>	12465081
Total FP	1159	<	3786
Total FP CONTRA	149	<	593
Total FP INCONS	828	<	3093
Total FP COMP	182	>	100
Total FN	1981	<	4294
P-value	0.0

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

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	0.013
Average MCC ± 95% Confidence Intervals	0.014 ± 0.011
Sensitivity	0.013
Positive Predictive Value	0.015
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...	0.01	0.01	0.01	4	1178459	419	57	360	2	469
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.00	0.00	0.00	0	1198499	431	60	367	4	478
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.04	0.04	0.05	19	1129855	384	58	324	2	431
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1117843	408	79	329	0	444
CRW_00330	SSU_rRNA_eukarya links to Rfam database...	0.02	0.02	0.02	8	1988575	477	82	350	45	509
CRW_00411	SSU_rRNA_eukarya links to Rfam database...	0.00	0.00	0.00	0	1615135	382	74	294	14	496
CRW_00414	SSU_rRNA_eukarya links to Rfam database...	0.01	0.01	0.01	3	1665773	466	78	371	17	492
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.02	0.02	0.02	9	1137394	389	58	325	6	438
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.01	0.01	0.01	3	1433548	430	47	373	10	537

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