CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RSpredict(20)
MCC	0.733	>	0.593
Average MCC ± 95% Confidence Intervals	0.687 ± 0.160	>	0.552 ± 0.142
Sensitivity	0.715	>	0.539
Positive Predictive Value	0.757	>	0.660
Total TP	293	>	221
Total TN	39357	<	39409
Total FP	165	>	159
Total FP CONTRA	43	>	36
Total FP INCONS	51	<	78
Total FP COMP	71	>	45
Total FN	117	<	189
P-value	2.71568867205e-08

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

Total Scores
MCC	0.733
Average MCC ± 95% Confidence Intervals	0.687 ± 0.160
Sensitivity	0.715
Positive Predictive Value	0.757
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J2L_3	5S_rRNA links to Rfam database...	0.95	0.91	1.00	31	2989	4	0	0	4	3
3J3D_C	tRNA links to Rfam database...	0.79	0.79	0.79	15	949	4	3	1	0	4
3J3E_7	5S_rRNA links to Rfam database...	0.94	0.88	1.00	30	2711	2	0	0	2	4
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2722	29	12	8	9	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.42	0.31	8	4735	32	9	9	14	11
3J3F_7	5S_rRNA links to Rfam database...	0.96	0.92	1.00	33	2901	2	0	0	2	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
3ZEX_D	5S_rRNA links to Rfam database...	0.92	0.86	1.00	30	2766	4	0	0	4	5
3ZND_W	tRNA links to Rfam database...	0.26	0.38	0.19	3	1175	22	6	7	9	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.96	0.92	1.00	34	2729	1	0	0	1	3
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7

Total Scores
MCC	0.593
Average MCC ± 95% Confidence Intervals	0.552 ± 0.142
Sensitivity	0.539
Positive Predictive Value	0.660
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.67	0.50	0.91	10	1101	2	0	1	1	10
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.59	0.87	20	2997	6	0	3	3	14
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_7	5S_rRNA links to Rfam database...	0.82	0.79	0.84	27	2709	7	0	5	2	7
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
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	3	1	1	1	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.31	0.38	9	5350	19	3	12	4	20
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	7	0	2	5	6
3ZND_W	tRNA links to Rfam database...	0.47	0.38	0.60	3	1186	9	0	2	7	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4A1C_3	5S_rRNA links to Rfam database...	0.60	0.49	0.75	18	2739	8	0	6	2	19
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.