CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(20)		Fold
MCC	0.521	>	0.470
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127	>	0.434 ± 0.163
Sensitivity	0.366	<	0.416
Positive Predictive Value	0.748	>	0.538
Total TP	163	<	185
Total TN	67962	>	67836
Total FP	61	<	188
Total FP CONTRA	4	<	15
Total FP INCONS	51	<	144
Total FP COMP	6	<	29
Total FN	282	>	260
P-value	1.70887622364e-08

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

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	0.470
Average MCC ± 95% Confidence Intervals	0.434 ± 0.163
Sensitivity	0.416
Positive Predictive Value	0.538
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...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.62	0.53	0.74	28	7837	12	0	10	2	25
3J3D_C	tRNA links to Rfam database...	0.47	0.43	0.52	12	2752	11	1	10	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7478	34	2	23	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.57	20	7105	15	1	14	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.28	0.29	10	12211	39	5	20	14	26
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3J3V_B	5S_rRNA links to Rfam database...	0.51	0.42	0.63	24	6983	14	1	13	0	33
3ZEX_D	5S_rRNA links to Rfam database...	0.76	0.67	0.87	33	6983	5	1	4	0	16
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.27	7	3460	19	3	16	0	25

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