CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidAlifold(20)		PETfold_pre2.0(20)
MCC	0.656	>	0.649
Average MCC ± 95% Confidence Intervals	0.626 ± 0.119	<	0.630 ± 0.114
Sensitivity	0.501	<	0.530
Positive Predictive Value	0.864	>	0.798
Total TP	344	<	364
Total TN	110797	>	110739
Total FP	65	<	120
Total FP CONTRA	4	=	4
Total FP INCONS	50	<	88
Total FP COMP	11	<	28
Total FN	343	>	323
P-value	1.64089763604e-07

Comparison of performance of CentroidAlifold(20) and PETfold_pre2.0(20). 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 CentroidAlifold(20) and PETfold_pre2.0(20)).
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 CentroidAlifold(20) and PETfold_pre2.0(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and PETfold_pre2.0(20). 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 CentroidAlifold(20) and PETfold_pre2.0(20)).

Total Scores
MCC	0.656
Average MCC ± 95% Confidence Intervals	0.626 ± 0.119
Sensitivity	0.501
Positive Predictive Value	0.864
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.76	0.58	1.00	31	7844	2	0	0	2	22
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7499	4	0	4	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	10	0	10	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.68	0.92	34	7223	4	0	3	1	16
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.25	0.60	9	12231	6	1	5	0	27
3J3V_B	5S_rRNA links to Rfam database...	0.66	0.47	0.93	27	6992	2	0	2	0	30
3ZEX_D	5S_rRNA links to Rfam database...	0.80	0.69	0.92	34	6984	3	0	3	0	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.21	0.69	11	14180	5	1	4	0	41
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	12	0	9	3	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4A1C_3	5S_rRNA links to Rfam database...	0.76	0.63	0.92	34	7103	4	0	3	1	20
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.53	0.89	17	3467	2	1	1	0	15

Total Scores
MCC	0.649
Average MCC ± 95% Confidence Intervals	0.630 ± 0.114
Sensitivity	0.530
Positive Predictive Value	0.798
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	9
3J2L_3	5S_rRNA links to Rfam database...	0.78	0.62	0.97	33	7841	3	0	1	2	20
3J3D_C	tRNA links to Rfam database...	0.80	0.68	0.95	19	2755	1	0	1	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.32	0.21	0.50	7	7489	11	0	7	4	26
3J3E_7	5S_rRNA links to Rfam database...	0.74	0.63	0.87	34	7101	5	1	4	0	20
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.68	0.89	34	7222	5	1	3	1	16
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.25	0.38	9	12222	22	0	15	7	27
3J3V_B	5S_rRNA links to Rfam database...	0.65	0.51	0.83	29	6986	6	1	5	0	28
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.71	0.92	35	6983	3	0	3	0	14
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.17	0.35	9	14170	18	0	17	1	43
3ZND_W	tRNA links to Rfam database...	0.47	0.43	0.53	10	2984	11	0	9	2	13
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.15	0.25	5	11761	25	0	15	10	28
4A1C_3	5S_rRNA links to Rfam database...	0.82	0.69	0.97	37	7102	1	0	1	0	17
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.61	0.42	0.89	8	1266	1	0	1	0	11
4ENC_A	crcB links to Rfam database...	0.55	0.42	0.73	8	1315	3	0	3	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.63	0.91	20	3464	2	1	1	0	12

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