CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		PPfold(seed)
MCC	0.346	>	0.125
Average MCC ± 95% Confidence Intervals	0.374 ± 0.176	>	0.078 ± 0.162
Sensitivity	0.353	>	0.030
Positive Predictive Value	0.349	<	0.538
Total TP	83	>	7
Total TN	32265	<	32490
Total FP	165	>	25
Total FP CONTRA	21	>	0
Total FP INCONS	134	>	6
Total FP COMP	10	<	19
Total FN	152	<	228
P-value	0.0

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

Total Scores
MCC	0.346
Average MCC ± 95% Confidence Intervals	0.374 ± 0.176
Sensitivity	0.353
Positive Predictive Value	0.349
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...	0.52	0.55	0.50	11	1518	11	0	11	0	9
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8

Total Scores
MCC	0.125
Average MCC ± 95% Confidence Intervals	0.078 ± 0.162
Sensitivity	0.030
Positive Predictive Value	0.538
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...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	4371	0	0	0	0	42
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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