CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		TurboFold(seed)
MCC	0.717	>	0.633
Average MCC ± 95% Confidence Intervals	0.707 ± 0.074	>	0.640 ± 0.098
Sensitivity	0.584	>	0.562
Positive Predictive Value	0.883	>	0.716
Total TP	136	>	131
Total TN	46930	>	46901
Total FP	20	<	57
Total FP CONTRA	3	<	11
Total FP INCONS	15	<	41
Total FP COMP	2	<	5
Total FN	97	<	102
P-value	7.20029949774e-10

Comparison of performance of CentroidAlifold(seed) and TurboFold(seed). 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 CentroidAlifold(seed) and TurboFold(seed)).
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 CentroidAlifold(seed) and TurboFold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and TurboFold(seed). 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 CentroidAlifold(seed) and TurboFold(seed)).

Total Scores
MCC	0.717
Average MCC ± 95% Confidence Intervals	0.707 ± 0.074
Sensitivity	0.584
Positive Predictive Value	0.883
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00210	RNaseP_arch links to Rfam database...	0.74	0.65	0.86	42	27212	9	0	7	2	23
RFA_00636	HDV_ribozyme links to Rfam database...	0.78	0.68	0.90	19	3984	2	2	0	0	9
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	2006	0	0	0	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00808	RydC links to Rfam database...	0.65	0.56	0.75	9	2004	3	1	2	0	7
RFA_00809	RydC links to Rfam database...	0.43	0.38	0.50	6	2133	6	0	6	0	10

Total Scores
MCC	0.633
Average MCC ± 95% Confidence Intervals	0.640 ± 0.098
Sensitivity	0.562
Positive Predictive Value	0.716
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00210	RNaseP_arch links to Rfam database...	0.71	0.68	0.75	44	27202	16	4	11	1	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	5	0	2	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	2	1	0	1	8
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	0	1	0	8
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.38	0.38	0.40	6	2130	9	1	8	0	10

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