CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		Afold
MCC	0.764	>	0.614
Average MCC ± 95% Confidence Intervals	0.770 ± 0.098	>	0.657 ± 0.153
Sensitivity	0.657	>	0.640
Positive Predictive Value	0.891	>	0.596
Total TP	301	>	293
Total TN	58252	>	58098
Total FP	99	<	315
Total FP CONTRA	20	<	62
Total FP INCONS	17	<	137
Total FP COMP	62	<	116
Total FN	157	<	165
P-value	3.13260312532e-08

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

Total Scores
MCC	0.764
Average MCC ± 95% Confidence Intervals	0.770 ± 0.098
Sensitivity	0.657
Positive Predictive Value	0.891
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.59	0.56	0.67	10	342	6	0	5	1	8
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	12	0	0	12	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.20	1.00	7	2038	4	0	0	4	28
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.67	0.52	0.88	49	25480	9	7	0	2	46
3IZF_C	5S_rRNA links to Rfam database...	0.91	0.89	0.94	31	2607	6	0	2	4	4
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3JYX_4	5_8S_rRNA links to Rfam database...	0.67	0.75	0.60	9	4741	9	5	1	3	3
3JYX_3	5S_rRNA links to Rfam database...	0.80	0.80	0.80	12	2363	23	0	3	20	3
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...	0.77	0.65	0.92	24	2252	6	1	1	4	13
3O58_2	5S_rRNA links to Rfam database...	0.93	0.94	0.94	29	2723	9	0	2	7	2
3O58_3	5_8S_rRNA links to Rfam database...	0.64	0.45	0.91	10	4753	2	1	0	1	12
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	5	4505	8	3	3	2	15
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6

Total Scores
MCC	0.614
Average MCC ± 95% Confidence Intervals	0.657 ± 0.153
Sensitivity	0.640
Positive Predictive Value	0.596
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3IZF_C	5S_rRNA links to Rfam database...	0.83	0.86	0.81	30	2603	11	0	7	4	5
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.67	0.63	10	2362	29	0	6	23	5
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_2	5S_rRNA links to Rfam database...	0.80	0.81	0.81	25	2723	14	0	6	8	6
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
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.