CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		RNAfold
MCC	0.779	>	0.711
Average MCC ± 95% Confidence Intervals	0.774 ± 0.092	>	0.689 ± 0.147
Sensitivity	0.659	<	0.721
Positive Predictive Value	0.921	>	0.701
Total TP	442	<	484
Total TN	413762	>	413552
Total FP	105	<	388
Total FP CONTRA	9	<	70
Total FP INCONS	29	<	136
Total FP COMP	67	<	182
Total FN	229	>	187
P-value	1.42300079339e-08

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

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	0.711
Average MCC ± 95% Confidence Intervals	0.689 ± 0.147
Sensitivity	0.721
Positive Predictive Value	0.701
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...	0.67	0.67	0.68	26	21283	25	7	5	13	13
RFA_00620	Telomerase-cil links to Rfam database...	0.64	0.62	0.67	24	21909	25	3	9	13	15
RFA_00626	rne5 links to Rfam database...	0.96	0.92	1.00	80	56536	25	0	0	25	7
RFA_00627	rne5 links to Rfam database...	0.72	0.69	0.75	60	56873	35	4	16	15	27
RFA_00628	rne5 links to Rfam database...	0.93	0.91	0.96	78	57210	29	0	3	26	8
RFA_00630	rne5 links to Rfam database...	0.66	0.66	0.66	57	56867	40	6	23	11	30
RFA_00814	R2_retro_el links to Rfam database...	0.79	0.80	0.77	33	25157	26	4	6	16	8
RFA_00815	R2_retro_el links to Rfam database...	0.65	0.71	0.60	29	24483	34	7	12	15	12
RFA_00816	R2_retro_el links to Rfam database...	0.59	0.66	0.53	27	23169	32	13	11	8	14
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21885	55	16	39	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.59	0.63	0.55	26	20254	31	10	11	10	15
RFA_00819	R2_retro_el links to Rfam database...	0.96	0.95	0.98	39	27926	31	0	1	30	2

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