CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(20)		RNAwolf
MCC	0.521	>	0.370
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127	>	0.388 ± 0.147
Sensitivity	0.366	>	0.346
Positive Predictive Value	0.748	>	0.403
Total TP	163	>	154
Total TN	67962	>	67798
Total FP	61	<	257
Total FP CONTRA	4	<	20
Total FP INCONS	51	<	208
Total FP COMP	6	<	29
Total FN	282	<	291
P-value	6.99051034341e-09

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

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127
Sensitivity	0.366
Positive Predictive Value	0.748
Nr of predictions	11

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
3J3V_B	5S_rRNA links to Rfam database...	0.38	0.21	0.71	12	7004	5	0	5	0	45
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	0.370
Average MCC ± 95% Confidence Intervals	0.388 ± 0.147
Sensitivity	0.346
Positive Predictive Value	0.403
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.40	0.40	0.41	12	2821	18	0	17	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.55	0.49	0.62	26	7833	18	0	16	2	27
3J3D_C	tRNA links to Rfam database...	0.79	0.75	0.84	21	2750	5	2	2	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.41	0.35	0.49	19	7101	20	1	19	0	35
3J3F_8	5_8S_rRNA links to Rfam database...	0.23	0.25	0.21	9	12204	45	5	28	12	27
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.20	0.23	10	7216	34	2	32	0	40
3J3V_B	5S_rRNA links to Rfam database...	0.43	0.37	0.51	21	6980	20	2	18	0	36
3ZEX_D	5S_rRNA links to Rfam database...	0.20	0.18	0.22	9	6980	32	3	29	0	40
3ZND_W	tRNA links to Rfam database...	0.50	0.48	0.52	11	2982	13	0	10	3	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.56	0.50	0.64	16	3461	10	1	8	1	16

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