CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CMfinder(20)		MCFold
MCC	0.539	>	0.378
Average MCC ± 95% Confidence Intervals	0.527 ± 0.138	>	0.367 ± 0.156
Sensitivity	0.389	<	0.392
Positive Predictive Value	0.751	>	0.373
Total TP	151	<	152
Total TN	60958	>	60751
Total FP	56	<	299
Total FP CONTRA	4	<	27
Total FP INCONS	46	<	229
Total FP COMP	6	<	43
Total FN	237	>	236
P-value	7.84765843136e-09

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

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.527 ± 0.138
Sensitivity	0.389
Positive Predictive Value	0.751
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...	0.75	0.57	1.00	17	2833	1	0	0	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	11	1	9	1	36
3J3D_C	tRNA links to Rfam database...	0.76	0.61	0.94	17	2757	1	0	1	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.06	0.17	2	7491	10	1	9	0	31
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.46	0.83	25	7110	5	1	4	0	29
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	8	1	7	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	6	0	5	1	24
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.39	0.86	19	6999	3	0	3	0	30
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.47	0.22	1.00	7	3479	0	0	0	0	25

Total Scores
MCC	0.378
Average MCC ± 95% Confidence Intervals	0.367 ± 0.156
Sensitivity	0.392
Positive Predictive Value	0.373
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...	0.59	0.57	0.63	17	2823	12	1	9	2	13
3J2L_3	5S_rRNA links to Rfam database...	0.58	0.57	0.60	30	7825	23	2	18	3	23
3J3D_C	tRNA links to Rfam database...	0.42	0.43	0.43	12	2747	18	2	14	2	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.12	0.12	4	7470	46	3	26	17	29
3J3E_7	5S_rRNA links to Rfam database...	0.40	0.39	0.42	21	7090	29	3	26	0	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.13	0.17	0.11	6	12191	61	9	40	12	30
3J3F_7	5S_rRNA links to Rfam database...	0.74	0.74	0.74	37	7210	17	2	11	4	13
3ZEX_D	5S_rRNA links to Rfam database...	0.17	0.18	0.18	9	6970	42	4	38	0	40
3ZND_W	tRNA links to Rfam database...	0.19	0.22	0.18	5	2975	26	1	22	3	18
4FRG_B	AdoCbl-variant links to Rfam database...	0.32	0.34	0.31	11	3450	25	0	25	0	21

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