CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		Afold
MCC	0.641	>	0.513
Average MCC ± 95% Confidence Intervals	0.639 ± 0.085	>	0.538 ± 0.132
Sensitivity	0.484	>	0.472
Positive Predictive Value	0.852	>	0.563
Total TP	317	>	309
Total TN	157530	>	157353
Total FP	83	<	299
Total FP CONTRA	13	<	39
Total FP INCONS	42	<	201
Total FP COMP	28	<	59
Total FN	338	<	346
P-value	2.34821445183e-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	0.641
Average MCC ± 95% Confidence Intervals	0.639 ± 0.085
Sensitivity	0.484
Positive Predictive Value	0.852
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...	0.61	0.55	0.69	11	974	5	0	5	0	9
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	11	5	3	3	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	8	5143	3	0	0	3	34
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3IZ4_A	tmRNA links to Rfam database...	0.58	0.39	0.88	51	70818	7	3	4	0	81
3IZF_C	5S_rRNA links to Rfam database...	0.75	0.61	0.92	33	6867	4	0	3	1	21
3JYV_7	tRNA links to Rfam database...	0.81	0.66	1.00	21	2829	0	0	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	9	12230	9	0	7	2	24
3JYX_3	5S_rRNA links to Rfam database...	0.61	0.56	0.68	15	6306	20	0	7	13	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.70	0.54	0.89	25	6993	5	1	2	2	21
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	9	2	5	2	9
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.31	0.92	11	12391	1	0	1	0	24
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10

Total Scores
MCC	0.513
Average MCC ± 95% Confidence Intervals	0.538 ± 0.132
Sensitivity	0.472
Positive Predictive Value	0.563
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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
3A2K_C	tRNA links to Rfam database...	0.41	0.39	0.44	11	2901	14	2	12	0	17
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IZ4_A	tmRNA links to Rfam database...	0.48	0.45	0.51	59	70760	58	11	46	1	73
3IZF_C	5S_rRNA links to Rfam database...	0.66	0.57	0.76	31	6862	10	1	9	0	23
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2827	23	1	22	0	32
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	35	5	17	13	23
3JYX_3	5S_rRNA links to Rfam database...	0.54	0.56	0.54	15	6300	24	1	12	11	12
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.74	0.61	0.90	28	6990	5	0	3	2	18
3O58_2	5S_rRNA links to Rfam database...	0.66	0.66	0.66	25	7222	14	4	9	1	13
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

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