CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		RDfolder
MCC	0.495	>	0.460
Average MCC ± 95% Confidence Intervals	0.652 ± 0.195	>	0.608 ± 0.249
Sensitivity	0.493	>	0.378
Positive Predictive Value	0.510	<	0.572
Total TP	103	>	79
Total TN	16680	<	16744
Total FP	103	>	60
Total FP CONTRA	10	>	4
Total FP INCONS	89	>	55
Total FP COMP	4	>	1
Total FN	106	<	130
P-value	4.00862119973e-08

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

Total Scores
MCC	0.495
Average MCC ± 95% Confidence Intervals	0.652 ± 0.195
Sensitivity	0.493
Positive Predictive Value	0.510
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.17	0.18	0.18	7	4713	34	1	32	1	33
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ATO_G	-	0.61	0.70	0.54	7	515	6	2	4	0	3
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8
4HXH_A	-	0.81	1.00	0.67	6	316	3	3	0	0	0

Total Scores
MCC	0.460
Average MCC ± 95% Confidence Intervals	0.608 ± 0.249
Sensitivity	0.378
Positive Predictive Value	0.572
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ATO_G	-	0.63	0.40	1.00	4	524	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13
4HXH_A	-	1.00	1.00	1.00	6	319	0	0	0	0	0

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