CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		RSpredict(20)
MCC	0.856	>	0.625
Average MCC ± 95% Confidence Intervals	0.846 ± 0.067	>	0.558 ± 0.134
Sensitivity	0.817	>	0.568
Positive Predictive Value	0.897	>	0.690
Total TP	531	>	369
Total TN	199834	<	199891
Total FP	187	<	240
Total FP CONTRA	18	<	50
Total FP INCONS	43	<	116
Total FP COMP	126	>	74
Total FN	119	<	281
P-value	2.66715895098e-08

Comparison of performance of PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) 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 PETfold_pre2.0(seed) and RSpredict(20)).

Total Scores
MCC	0.856
Average MCC ± 95% Confidence Intervals	0.846 ± 0.067
Sensitivity	0.817
Positive Predictive Value	0.897
Nr of predictions	18

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	2	0	0	2	0
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.86	180	160472	78	7	23	48	60
3J2L_3	5S_rRNA links to Rfam database...	0.97	0.94	1.00	32	2988	5	0	0	5	2
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	4	3	0	1	1
3J3E_7	5S_rRNA links to Rfam database...	0.97	0.97	0.97	33	2707	6	0	1	5	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.71	0.67	0.77	10	2729	8	1	2	5	5
3J3F_8	5_8S_rRNA links to Rfam database...	0.86	0.84	0.89	16	4743	13	2	0	11	3
3J3F_7	5S_rRNA links to Rfam database...	0.99	0.97	1.00	35	2899	4	0	0	4	1
3ZEX_D	5S_rRNA links to Rfam database...	0.96	0.94	0.97	33	2762	6	0	1	5	2
3ZEX_C	5_8S_rRNA links to Rfam database...	0.70	0.59	0.85	17	5354	12	1	2	9	12
3ZND_W	tRNA links to Rfam database...	0.67	0.75	0.60	6	1181	16	0	4	12	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
4A1C_3	5S_rRNA links to Rfam database...	1.00	1.00	1.00	37	2726	2	0	0	2	0
4AOB_A	SAM links to Rfam database...	0.85	0.79	0.92	23	1412	4	0	2	2	6
4ENB_A	crcB links to Rfam database...	0.61	0.53	0.73	8	461	5	1	2	2	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	5	1	2	2	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.87	0.83	0.91	20	1180	3	0	2	1	4

Total Scores
MCC	0.625
Average MCC ± 95% Confidence Intervals	0.558 ± 0.134
Sensitivity	0.568
Positive Predictive Value	0.690
Nr of predictions	18

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
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.68	0.62	0.74	148	160482	81	14	38	29	92
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_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	7	0	2	5	6
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.31	0.38	9	5350	19	3	12	4	20
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.