CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(20)		CentroidFold
MCC	0.648	>	0.645
Average MCC ± 95% Confidence Intervals	0.625 ± 0.138	>	0.594 ± 0.169
Sensitivity	0.563	<	0.680
Positive Predictive Value	0.754	>	0.619
Total TP	153	<	185
Total TN	26027	>	25931
Total FP	71	<	168
Total FP CONTRA	15	<	39
Total FP INCONS	35	<	75
Total FP COMP	21	<	54
Total FN	119	>	87
P-value	0.00868291460752

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

Total Scores
MCC	0.648
Average MCC ± 95% Confidence Intervals	0.625 ± 0.138
Sensitivity	0.563
Positive Predictive Value	0.754
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...	0.84	0.76	0.94	16	1202	2	1	0	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.57	0.50	0.65	17	2994	11	2	7	2	17
3J3D_C	tRNA links to Rfam database...	0.81	0.79	0.83	15	950	3	3	0	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.13	0.17	2	2730	10	3	7	0	13
3J3E_7	5S_rRNA links to Rfam database...	0.81	0.74	0.89	25	2713	5	0	3	2	9
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	9	4743	11	5	4	2	10
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.72	0.87	26	2904	6	1	3	2	10
3J3V_B	5S_rRNA links to Rfam database...	0.53	0.41	0.69	11	2640	6	0	5	1	16
3ZEX_D	5S_rRNA links to Rfam database...	0.70	0.54	0.90	19	2775	3	0	2	1	16
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	14	0	4	10	2
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.29	1.00	7	1195	0	0	0	0	17

Total Scores
MCC	0.645
Average MCC ± 95% Confidence Intervals	0.594 ± 0.169
Sensitivity	0.680
Positive Predictive Value	0.619
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...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.76	0.72	26	2984	15	1	9	5	8
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.13	0.13	2	2726	22	4	10	8	13
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.59	0.65	20	2710	13	2	9	2	14
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	37	12	11	14	10
3J3F_7	5S_rRNA links to Rfam database...	0.84	0.86	0.82	31	2896	9	1	6	2	5
3J3V_B	5S_rRNA links to Rfam database...	0.72	0.74	0.71	20	2628	16	1	7	8	7
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.86	0.91	30	2763	8	0	3	5	5
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7

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