CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CMfinder(20)		RSpredict(seed)
MCC	0.660	>	0.017
Average MCC ± 95% Confidence Intervals	0.635 ± 0.153	>	0.014 ± 0.043
Sensitivity	0.580	>	0.008
Positive Predictive Value	0.759	>	0.054
Total TP	142	>	2
Total TN	23387	<	23537
Total FP	65	>	38
Total FP CONTRA	15	>	6
Total FP INCONS	30	>	29
Total FP COMP	20	>	3
Total FN	103	<	243
P-value	1.03576421863e-08

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

Total Scores
MCC	0.660
Average MCC ± 95% Confidence Intervals	0.635 ± 0.153
Sensitivity	0.580
Positive Predictive Value	0.759
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...	0.84	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
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	0.017
Average MCC ± 95% Confidence Intervals	0.014 ± 0.043
Sensitivity	0.008
Positive Predictive Value	0.054
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...	-0.01	0.00	0.00	0	1215	4	0	4	0	21
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3015	5	0	5	0	34
3J3D_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	964	4	1	3	0	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3E_7	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2733	8	1	7	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	5	3	1	1	17
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2930	4	1	3	0	36
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2794	2	0	2	0	35
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	1189	4	0	2	2	8
4FRG_B	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	1200	2	0	2	0	24

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