CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	TurboFold(seed)		RNAfold
MCC	0.600	>	0.464
Average MCC ± 95% Confidence Intervals	0.632 ± 0.110	>	0.465 ± 0.155
Sensitivity	0.518	>	0.452
Positive Predictive Value	0.702	>	0.484
Total TP	87	>	76
Total TN	19699	>	19666
Total FP	41	<	87
Total FP CONTRA	7	<	15
Total FP INCONS	30	<	66
Total FP COMP	4	<	6
Total FN	81	<	92
P-value	0.0

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

Total Scores
MCC	0.600
Average MCC ± 95% Confidence Intervals	0.632 ± 0.110
Sensitivity	0.518
Positive Predictive Value	0.702
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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

Total Scores
MCC	0.464
Average MCC ± 95% Confidence Intervals	0.465 ± 0.155
Sensitivity	0.452
Positive Predictive Value	0.484
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	7	1	6	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.52	0.56	0.50	10	1933	10	4	6	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...	0.55	0.56	0.56	10	1935	8	2	6	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	18	2	13	3	16
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	11	1	10	0	10

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