CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		Carnac(seed)
MCC	0.289	>	0.273
Average MCC ± 95% Confidence Intervals	0.316 ± 0.172	>	0.136 ± 0.218
Sensitivity	0.308	>	0.075
Positive Predictive Value	0.279	<	1.000
Total TP	95	>	23
Total TN	53170	<	53487
Total FP	278	>	0
Total FP CONTRA	36	>	0
Total FP INCONS	209	>	0
Total FP COMP	33	>	0
Total FN	213	<	285
P-value	0.0

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

Total Scores
MCC	0.289
Average MCC ± 95% Confidence Intervals	0.316 ± 0.172
Sensitivity	0.308
Positive Predictive Value	0.279
Nr of predictions	9

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
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7466	47	6	31	10	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.22	12	12192	54	9	33	12	24
3W3S_B	tRNA-Sec links to Rfam database...	0.17	0.18	0.18	7	4713	34	1	32	1	33
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
4JF2_A	preQ1-II links to Rfam database...	0.51	0.55	0.49	17	2815	18	5	13	0	14

Total Scores
MCC	0.273
Average MCC ± 95% Confidence Intervals	0.136 ± 0.218
Sensitivity	0.075
Positive Predictive Value	1.000
Nr of predictions	9

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...	0.44	0.20	1.00	4	1536	0	0	0	0	16
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12246	0	0	0	0	36
3W3S_B	tRNA-Sec links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	40
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...	0.00	0.00	0.00	0	11781	0	0	0	0	33
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
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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