CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Sfold		RSpredict(20)
MCC	0.609	>	0.585
Average MCC ± 95% Confidence Intervals	0.589 ± 0.124	>	0.564 ± 0.144
Sensitivity	0.583	>	0.534
Positive Predictive Value	0.642	<	0.649
Total TP	339	>	310
Total TN	68001	<	68051
Total FP	268	>	210
Total FP CONTRA	61	<	73
Total FP INCONS	128	>	95
Total FP COMP	79	>	42
Total FN	242	<	271
P-value	1.18380060481e-06

Comparison of performance of Sfold and RSpredict(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 Sfold and RSpredict(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 Sfold and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and RSpredict(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 Sfold and RSpredict(20)).

Total Scores
MCC	0.609
Average MCC ± 95% Confidence Intervals	0.589 ± 0.124
Sensitivity	0.583
Positive Predictive Value	0.642
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3GX2_A	SAM links to Rfam database...	0.86	0.79	0.96	22	1426	2	1	0	1	6
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...	0.59	0.56	0.63	53	25452	34	14	17	3	42
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J3D_C	tRNA links to Rfam database...	0.44	0.37	0.54	7	955	6	1	5	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.08	2	2718	32	6	16	10	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.33	9	4734	37	8	10	19	10
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1095	16	2	14	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...	0.85	0.78	0.94	29	2247	7	0	2	5	8
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	18	2	8	8	11
3PDR_A	ykoK links to Rfam database...	0.82	0.80	0.85	40	4793	9	2	5	2	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.78	0.72	0.84	21	1508	4	2	2	0	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.34	0.50	10	5354	27	2	8	17	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.67	0.58	0.78	14	1184	4	3	1	0	10

Total Scores
MCC	0.585
Average MCC ± 95% Confidence Intervals	0.564 ± 0.144
Sensitivity	0.534
Positive Predictive Value	0.649
Nr of predictions	21

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3A2K_C	tRNA links to Rfam database...	0.88	0.86	0.90	19	1087	2	0	2	0	3
3GX2_A	SAM links to Rfam database...	0.40	0.21	0.75	6	1441	2	1	1	0	22
3IVN_B	Purine links to Rfam database...	0.91	0.87	0.95	20	882	1	1	0	0	3
3IZ4_A	tmRNA links to Rfam database...	0.61	0.57	0.67	54	25455	38	13	14	11	41
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	19	5	13	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.47	0.38	9	4737	26	9	6	11	10
3JYV_7	tRNA links to Rfam database...	0.97	0.95	1.00	19	1092	2	0	0	2	1
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2272	6	1	5	0	37
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.30	11	4727	29	15	11	3	11
3PDR_A	ykoK links to Rfam database...	0.80	0.70	0.92	35	4802	5	1	2	2	15
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	1	0	0	3
3SD1_A	THF links to Rfam database...	0.82	0.86	0.78	25	1501	7	5	2	0	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.31	0.38	9	5350	19	3	12	4	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4AOB_A	SAM links to Rfam database...	0.33	0.21	0.55	6	1426	5	1	4	0	23
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.51	0.40	0.67	6	487	3	0	3	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.13	0.33	3	1193	6	1	5	0	21

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