CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		CentroidAlifold(20)
MCC	0.803	>	0.672
Average MCC ± 95% Confidence Intervals	0.787 ± 0.086	>	0.622 ± 0.220
Sensitivity	0.752	>	0.558
Positive Predictive Value	0.861	>	0.816
Total TP	155	>	115
Total TN	23007	<	23046
Total FP	68	>	36
Total FP CONTRA	11	<	12
Total FP INCONS	14	=	14
Total FP COMP	43	>	10
Total FN	51	<	91
P-value	6.35199149577e-09

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

Total Scores
MCC	0.803
Average MCC ± 95% Confidence Intervals	0.787 ± 0.086
Sensitivity	0.752
Positive Predictive Value	0.861
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
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
3J3F_8	5_8S_rRNA links to Rfam database...	0.86	0.84	0.89	16	4743	13	2	0	11	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.70	0.59	0.85	17	5354	12	1	2	9	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.79	0.75	0.83	15	4498	12	1	2	9	5
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	0.672
Average MCC ± 95% Confidence Intervals	0.622 ± 0.220
Sensitivity	0.558
Positive Predictive Value	0.816
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
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...	0.00	0.00	0.00	0	2738	4	1	3	0	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.37	0.54	7	4748	8	3	3	2	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.31	0.64	9	5360	7	1	4	2	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	5	4505	8	3	3	2	15
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
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...	0.68	0.47	1.00	7	489	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.71	0.94	17	1184	2	0	1	1	7

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