CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	RNAshapes		NanoFolder
MCC	0.455	>	0.304
Average MCC ± 95% Confidence Intervals	0.461 ± 0.287	>	0.353 ± 0.351
Sensitivity	0.416	>	0.343
Positive Predictive Value	0.507	>	0.281
Total TP	69	>	57
Total TN	18893	>	18826
Total FP	73	<	159
Total FP CONTRA	14	<	22
Total FP INCONS	53	<	124
Total FP COMP	6	<	13
Total FN	97	<	109
P-value	0.0

Comparison of performance of RNAshapes and NanoFolder. 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 RNAshapes and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAshapes and NanoFolder. 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 RNAshapes and NanoFolder).

Total Scores
MCC	0.455
Average MCC ± 95% Confidence Intervals	0.461 ± 0.287
Sensitivity	0.416
Positive Predictive Value	0.507
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00571	tRNA links to Rfam database...	0.17	0.16	0.19	4	3300	17	6	11	0	21
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00851	-	0.35	0.29	0.43	12	4725	16	0	16	0	29
PDB_01009	tRNA links to Rfam database...	0.52	0.57	0.48	12	2460	13	5	8	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	2001	8	0	5	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	15	2	13	0	16

Total Scores
MCC	0.304
Average MCC ± 95% Confidence Intervals	0.353 ± 0.351
Sensitivity	0.343
Positive Predictive Value	0.281
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00571	tRNA links to Rfam database...	-0.01	0.00	0.00	0	3286	36	6	29	1	25
PDB_00828	Purine links to Rfam database...	0.30	0.33	0.28	9	2453	23	0	23	0	18
PDB_00851	-	0.16	0.17	0.17	7	4711	35	3	32	0	34
PDB_01009	tRNA links to Rfam database...	0.27	0.33	0.23	7	2455	25	3	20	2	14
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1996	24	0	20	4	18
RFA_00773	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1932	9	3	0	6	0
RFA_00808	RydC links to Rfam database...	0.83	1.00	0.70	16	1993	7	7	0	0	0

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