CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		Afold
MCC	0.670	>	0.539
Average MCC ± 95% Confidence Intervals	0.639 ± 0.128	>	0.590 ± 0.166
Sensitivity	0.528	<	0.585
Positive Predictive Value	0.856	>	0.504
Total TP	249	<	276
Total TN	72400	>	72143
Total FP	66	<	342
Total FP CONTRA	37	<	110
Total FP INCONS	5	<	162
Total FP COMP	24	<	70
Total FN	223	>	196
P-value	2.7402423548e-08

Comparison of performance of CentroidAlifold(seed) and Afold. 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(seed) and Afold).
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(seed) and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and Afold. 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(seed) and Afold).

Total Scores
MCC	0.670
Average MCC ± 95% Confidence Intervals	0.639 ± 0.128
Sensitivity	0.528
Positive Predictive Value	0.856
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	528	0	0	0	0	18
2ZZN_D	tRNA links to Rfam database...	0.52	0.27	1.00	6	978	0	0	0	0	16
3A2K_C	tRNA links to Rfam database...	0.52	0.27	1.00	6	1102	0	0	0	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.56	0.55	0.57	28	22391	30	19	2	9	23
3IZ4_A	tmRNA links to Rfam database...	0.58	0.43	0.77	41	25483	17	12	0	5	54
3J3E_8	5_8S_rRNA links to Rfam database...	0.39	0.20	0.75	3	2738	1	1	0	0	12
3JYV_7	tRNA links to Rfam database...	0.50	0.25	1.00	5	1106	1	0	0	1	15
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.79	0.65	0.96	24	2253	5	0	1	4	13
3O58_3	5_8S_rRNA links to Rfam database...	0.68	0.50	0.92	11	4752	2	1	0	1	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.70	0.92	23	1964	4	0	2	2	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4ENB_A	crcB links to Rfam database...	0.72	0.53	1.00	8	464	0	0	0	0	7

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.590 ± 0.166
Sensitivity	0.585
Positive Predictive Value	0.504
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
2ZZN_D	tRNA links to Rfam database...	0.91	0.91	0.91	20	962	3	2	0	1	2
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

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