CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		RSpredict(seed)
MCC	0.412	>	0.108
Average MCC ± 95% Confidence Intervals	0.427 ± 0.199	>	0.101 ± 0.176
Sensitivity	0.506	>	0.058
Positive Predictive Value	0.350	>	0.225
Total TP	79	>	9
Total TN	11966	<	12152
Total FP	169	>	32
Total FP CONTRA	52	>	7
Total FP INCONS	95	>	24
Total FP COMP	22	>	1
Total FN	77	<	147
P-value	0.0

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

Total Scores
MCC	0.412
Average MCC ± 95% Confidence Intervals	0.427 ± 0.199
Sensitivity	0.506
Positive Predictive Value	0.350
Nr of predictions	7

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...	0.54	0.61	0.50	11	506	11	1	10	0	7
3J16_L	tRNA links to Rfam database...	0.43	0.52	0.37	11	1129	19	8	11	0	10
3UZL_B	tRNA links to Rfam database...	0.41	0.56	0.31	9	1264	25	10	10	5	7
4A1C_3	5S_rRNA links to Rfam database...	0.58	0.68	0.51	25	2714	24	9	15	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	4469	61	18	29	14	20
4AOB_A	SAM links to Rfam database...	0.39	0.41	0.39	12	1406	20	4	15	1	17
4ENC_A	crcB links to Rfam database...	0.66	0.73	0.61	11	478	9	2	5	2	4

Total Scores
MCC	0.108
Average MCC ± 95% Confidence Intervals	0.101 ± 0.176
Sensitivity	0.058
Positive Predictive Value	0.225
Nr of predictions	7

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...	-0.03	0.00	0.00	0	515	13	0	13	0	18
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3UZL_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1287	6	3	3	0	16
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12

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