CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		RNASampler(seed)
MCC	0.813	>	0.779
Average MCC ± 95% Confidence Intervals	0.794 ± 0.146	>	0.774 ± 0.092
Sensitivity	0.782	>	0.659
Positive Predictive Value	0.845	<	0.921
Total TP	525	>	442
Total TN	413621	<	413762
Total FP	314	>	105
Total FP CONTRA	29	>	9
Total FP INCONS	67	>	29
Total FP COMP	218	>	67
Total FN	146	<	229
P-value	2.08252958266e-08

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

Total Scores
MCC	0.813
Average MCC ± 95% Confidence Intervals	0.794 ± 0.146
Sensitivity	0.782
Positive Predictive Value	0.845
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...	0.53	0.51	0.56	20	21285	25	4	12	9	19
RFA_00620	Telomerase-cil links to Rfam database...	0.20	0.18	0.23	7	21915	33	7	16	10	32
RFA_00626	rne5 links to Rfam database...	0.89	0.87	0.92	76	56533	29	2	5	22	11
RFA_00627	rne5 links to Rfam database...	0.83	0.79	0.87	69	56874	36	1	9	26	18
RFA_00628	rne5 links to Rfam database...	0.85	0.81	0.89	70	57212	38	2	7	29	16
RFA_00630	rne5 links to Rfam database...	0.82	0.78	0.86	68	56874	33	2	9	22	19
RFA_00814	R2_retro_el links to Rfam database...	0.95	0.93	0.97	38	25161	22	0	1	21	3
RFA_00815	R2_retro_el links to Rfam database...	0.96	0.93	1.00	38	24493	15	0	0	15	3
RFA_00816	R2_retro_el links to Rfam database...	0.96	0.93	1.00	38	23182	15	0	0	15	3
RFA_00817	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	21909	12	0	0	12	5
RFA_00818	R2_retro_el links to Rfam database...	0.64	0.68	0.61	28	20255	30	11	7	12	13
RFA_00819	R2_retro_el links to Rfam database...	0.94	0.90	0.97	37	27928	26	0	1	25	4

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

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