CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		RDfolder
MCC	0.737	>	0.489
Average MCC ± 95% Confidence Intervals	0.722 ± 0.093	>	0.486 ± 0.186
Sensitivity	0.585	>	0.365
Positive Predictive Value	0.934	>	0.667
Total TP	141	>	88
Total TN	21576	<	21595
Total FP	12	<	48
Total FP CONTRA	0	<	3
Total FP INCONS	10	<	41
Total FP COMP	2	<	4
Total FN	100	<	153
P-value	0.0

Comparison of performance of PPfold(20) and RDfolder. 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 PPfold(20) and RDfolder).
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 PPfold(20) and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and RDfolder. 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 PPfold(20) and RDfolder).

Total Scores
MCC	0.737
Average MCC ± 95% Confidence Intervals	0.722 ± 0.093
Sensitivity	0.585
Positive Predictive Value	0.934
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3J20_0	tRNA links to Rfam database...	0.84	0.70	1.00	21	2829	0	0	0	0	9
3J3D_C	tRNA links to Rfam database...	0.80	0.68	0.95	19	2755	1	0	1	0	9
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11

Total Scores
MCC	0.489
Average MCC ± 95% Confidence Intervals	0.486 ± 0.186
Sensitivity	0.365
Positive Predictive Value	0.667
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3J20_0	tRNA links to Rfam database...	0.73	0.57	0.94	17	2832	2	0	1	1	13
3J3D_C	tRNA links to Rfam database...	0.72	0.61	0.85	17	2755	3	0	3	0	11
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.30	0.17	0.54	7	3903	6	0	6	0	35
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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