CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(20)		Vsfold5
MCC	0.521	>	0.355
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127	>	0.375 ± 0.147
Sensitivity	0.366	>	0.299
Positive Predictive Value	0.748	>	0.430
Total TP	163	>	133
Total TN	67962	>	67871
Total FP	61	<	200
Total FP CONTRA	4	<	17
Total FP INCONS	51	<	159
Total FP COMP	6	<	24
Total FN	282	<	312
P-value	9.64686604905e-09

Comparison of performance of CMfinder(20) and Vsfold5. 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 Vsfold5).
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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for CMfinder(20) and Vsfold5. 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 Vsfold5).

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	0.355
Average MCC ± 95% Confidence Intervals	0.375 ± 0.147
Sensitivity	0.299
Positive Predictive Value	0.430
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...	0.67	0.57	0.81	17	2829	5	1	3	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.45	0.71	24	7841	13	1	9	3	29
3J3D_C	tRNA links to Rfam database...	0.60	0.54	0.68	15	2753	7	0	7	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.06	0.06	0.08	2	7477	31	5	19	7	31
3J3E_7	5S_rRNA links to Rfam database...	0.47	0.37	0.61	20	7107	13	0	13	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.33	12	12210	35	5	19	11	24
3J3F_7	5S_rRNA links to Rfam database...	0.21	0.18	0.26	9	7226	25	1	24	0	41
3J3V_B	5S_rRNA links to Rfam database...	0.16	0.12	0.21	7	6988	26	1	25	0	50
3ZEX_D	5S_rRNA links to Rfam database...	0.08	0.06	0.11	3	6994	24	0	24	0	46
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...	0.56	0.47	0.68	15	3464	7	1	6	0	17

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