CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CMfinder(20)		Multilign(20)
MCC	0.539	>	0.502
Average MCC ± 95% Confidence Intervals	0.527 ± 0.138	>	0.477 ± 0.188
Sensitivity	0.389	<	0.418
Positive Predictive Value	0.751	>	0.609
Total TP	151	<	162
Total TN	60958	>	60893
Total FP	56	<	121
Total FP CONTRA	4	<	11
Total FP INCONS	46	<	93
Total FP COMP	6	<	17
Total FN	237	>	226
P-value	1.5677163434e-08

Comparison of performance of CMfinder(20) and Multilign(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 CMfinder(20) and Multilign(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 CMfinder(20) and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CMfinder(20) and Multilign(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 CMfinder(20) and Multilign(20)).

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.527 ± 0.138
Sensitivity	0.389
Positive Predictive Value	0.751
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.75	0.57	1.00	17	2833	1	0	0	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	11	1	9	1	36
3J3D_C	tRNA links to Rfam database...	0.76	0.61	0.94	17	2757	1	0	1	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.06	0.17	2	7491	10	1	9	0	31
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.46	0.83	25	7110	5	1	4	0	29
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	8	1	7	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	6	0	5	1	24
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.39	0.86	19	6999	3	0	3	0	30
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.47	0.22	1.00	7	3479	0	0	0	0	25

Total Scores
MCC	0.502
Average MCC ± 95% Confidence Intervals	0.477 ± 0.188
Sensitivity	0.418
Positive Predictive Value	0.609
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.61	0.53	0.70	16	2827	8	1	6	1	14
3J2L_3	5S_rRNA links to Rfam database...	0.65	0.53	0.80	28	7840	9	0	7	2	25
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7481	22	6	16	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.58	0.48	0.70	26	7103	11	0	11	0	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.41	0.36	0.46	13	12218	27	1	14	12	23
3J3F_7	5S_rRNA links to Rfam database...	0.43	0.30	0.63	15	7236	9	0	9	0	35
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	1	4	0	17
3ZND_W	tRNA links to Rfam database...	0.41	0.39	0.43	9	2982	14	2	10	2	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.12	0.09	0.17	3	3468	15	0	15	0	29

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