CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		CRWrnafold
MCC	0.779	>	0.474
Average MCC ± 95% Confidence Intervals	0.774 ± 0.092	>	0.421 ± 0.163
Sensitivity	0.659	>	0.499
Positive Predictive Value	0.921	>	0.452
Total TP	442	>	335
Total TN	413762	>	413501
Total FP	105	<	560
Total FP CONTRA	9	<	119
Total FP INCONS	29	<	287
Total FP COMP	67	<	154
Total FN	229	<	336
P-value	2.10198558684e-08

Comparison of performance of RNASampler(seed) and CRWrnafold. 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 RNASampler(seed) and CRWrnafold).
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 RNASampler(seed) and CRWrnafold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(seed) and CRWrnafold. 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 RNASampler(seed) and CRWrnafold).

Total Scores
MCC	0.779
Average MCC ± 95% Confidence Intervals	0.774 ± 0.092
Sensitivity	0.659
Positive Predictive Value	0.921
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00606	Telomerase-cil links to Rfam database...	0.44	0.36	0.54	14	21295	18	7	5	6	25
RFA_00620	Telomerase-cil links to Rfam database...	0.52	0.44	0.63	17	21918	15	2	8	5	22
RFA_00626	rne5 links to Rfam database...	0.80	0.64	1.00	56	56560	5	0	0	5	31
RFA_00627	rne5 links to Rfam database...	0.77	0.63	0.93	55	56894	8	0	4	4	32
RFA_00628	rne5 links to Rfam database...	0.78	0.64	0.95	55	57233	12	0	3	9	31
RFA_00630	rne5 links to Rfam database...	0.77	0.66	0.90	57	56890	15	0	6	9	30
RFA_00814	R2_retro_el links to Rfam database...	0.87	0.78	0.97	32	25167	6	0	1	5	9
RFA_00815	R2_retro_el links to Rfam database...	0.88	0.78	1.00	32	24499	8	0	0	8	9
RFA_00816	R2_retro_el links to Rfam database...	0.86	0.76	0.97	31	23188	6	0	1	5	10
RFA_00817	R2_retro_el links to Rfam database...	0.86	0.76	0.97	31	21913	1	0	1	0	10
RFA_00818	R2_retro_el links to Rfam database...	0.86	0.73	1.00	30	20271	6	0	0	6	11
RFA_00819	R2_retro_el links to Rfam database...	0.88	0.78	1.00	32	27934	5	0	0	5	9

Total Scores
MCC	0.474
Average MCC ± 95% Confidence Intervals	0.421 ± 0.163
Sensitivity	0.499
Positive Predictive Value	0.452
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00606	Telomerase-cil links to Rfam database...	0.41	0.46	0.37	18	21272	38	17	14	7	21
RFA_00620	Telomerase-cil links to Rfam database...	0.55	0.59	0.51	23	21900	40	4	18	18	16
RFA_00626	rne5 links to Rfam database...	0.64	0.63	0.65	55	56532	42	8	21	13	32
RFA_00627	rne5 links to Rfam database...	0.65	0.63	0.67	55	56871	42	6	21	15	32
RFA_00628	rne5 links to Rfam database...	0.89	0.85	0.94	73	57213	30	0	5	25	13
RFA_00630	rne5 links to Rfam database...	0.57	0.57	0.57	50	56865	51	12	26	13	37
RFA_00814	R2_retro_el links to Rfam database...	0.24	0.27	0.21	11	25148	48	10	31	7	30
RFA_00815	R2_retro_el links to Rfam database...	0.36	0.41	0.31	17	24477	49	6	31	12	24
RFA_00816	R2_retro_el links to Rfam database...	0.21	0.24	0.19	10	23166	50	20	24	6	31
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21883	57	17	40	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	20249	56	19	33	4	41
RFA_00819	R2_retro_el links to Rfam database...	0.44	0.44	0.44	18	27925	57	0	23	34	23

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