CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	RNASampler(seed)		McQFold
MCC	0.779	>	0.446
Average MCC ± 95% Confidence Intervals	0.774 ± 0.092	>	0.454 ± 0.127
Sensitivity	0.659	>	0.452
Positive Predictive Value	0.921	>	0.442
Total TP	442	>	303
Total TN	413762	>	413557
Total FP	105	<	464
Total FP CONTRA	9	<	87
Total FP INCONS	29	<	295
Total FP COMP	67	<	82
Total FN	229	<	368
P-value	1.80908287419e-08

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

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	0.446
Average MCC ± 95% Confidence Intervals	0.454 ± 0.127
Sensitivity	0.452
Positive Predictive Value	0.442
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...	0.32	0.33	0.32	13	21280	34	12	16	6	26
RFA_00620	Telomerase-cil links to Rfam database...	0.36	0.38	0.34	15	21901	37	4	25	8	24
RFA_00626	rne5 links to Rfam database...	0.21	0.22	0.21	19	56526	76	15	56	5	68
RFA_00627	rne5 links to Rfam database...	0.42	0.40	0.44	35	56873	47	13	32	2	52
RFA_00628	rne5 links to Rfam database...	0.42	0.41	0.43	35	57209	50	7	40	3	51
RFA_00630	rne5 links to Rfam database...	0.63	0.63	0.63	55	56865	41	6	27	8	32
RFA_00814	R2_retro_el links to Rfam database...	0.79	0.80	0.77	33	25157	21	0	10	11	8
RFA_00815	R2_retro_el links to Rfam database...	0.56	0.59	0.53	24	24486	27	1	20	6	17
RFA_00816	R2_retro_el links to Rfam database...	0.82	0.85	0.80	35	23176	12	4	5	3	6
RFA_00817	R2_retro_el links to Rfam database...	0.35	0.39	0.31	16	21894	39	9	26	4	25
RFA_00818	R2_retro_el links to Rfam database...	0.28	0.27	0.29	11	20263	30	12	15	3	30
RFA_00819	R2_retro_el links to Rfam database...	0.30	0.29	0.31	12	27927	50	4	23	23	29

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