CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		RNASampler(20)
MCC	0.887	>	0.689
Average MCC ± 95% Confidence Intervals	0.851 ± 0.067	>	0.678 ± 0.121
Sensitivity	0.858	>	0.643
Positive Predictive Value	0.919	>	0.745
Total TP	375	>	281
Total TN	41992	<	42023
Total FP	123	<	153
Total FP CONTRA	11	<	28
Total FP INCONS	22	<	68
Total FP COMP	90	>	57
Total FN	62	<	156
P-value	1.70887622364e-08

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

Total Scores
MCC	0.887
Average MCC ± 95% Confidence Intervals	0.851 ± 0.067
Sensitivity	0.858
Positive Predictive Value	0.919
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
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_8	5_8S_rRNA links to Rfam database...	0.71	0.67	0.77	10	2729	8	1	2	5	5
3J3E_7	5S_rRNA links to Rfam database...	0.97	0.97	0.97	33	2707	6	0	1	5	1
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
3J3V_B	5S_rRNA links to Rfam database...	0.90	0.89	0.92	24	2630	14	0	2	12	3
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	0.689
Average MCC ± 95% Confidence Intervals	0.678 ± 0.121
Sensitivity	0.643
Positive Predictive Value	0.745
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	1	0	0	1	0
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...	0.56	0.50	0.63	17	2993	12	3	7	2	17
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	21	5	8	8	12
3J3E_7	5S_rRNA links to Rfam database...	0.80	0.76	0.84	26	2710	6	0	5	1	8
3J3F_8	5_8S_rRNA links to Rfam database...	0.43	0.47	0.39	9	4738	20	6	8	6	10
3J3F_7	5S_rRNA links to Rfam database...	0.78	0.72	0.84	26	2903	5	0	5	0	10
3J3V_B	5S_rRNA links to Rfam database...	0.88	0.78	1.00	21	2635	4	0	0	4	6
3ZEX_D	5S_rRNA links to Rfam database...	0.83	0.69	1.00	24	2772	1	0	0	1	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.39	9	5351	21	3	11	7	20
3ZND_W	tRNA links to Rfam database...	0.58	0.75	0.46	6	1178	18	4	3	11	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.81	1.00	30	2733	0	0	0	0	7
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.64	0.54	0.76	13	1185	4	0	4	0	11

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