CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		NanoFolder
MCC	0.488	>	0.253
Average MCC ± 95% Confidence Intervals	0.428 ± 0.239	>	0.295 ± 0.192
Sensitivity	0.280	>	0.276
Positive Predictive Value	0.855	>	0.241
Total TP	71	>	70
Total TN	46287	>	46079
Total FP	16	<	254
Total FP CONTRA	0	<	34
Total FP INCONS	12	<	187
Total FP COMP	4	<	33
Total FN	183	<	184
P-value	0.0

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

Total Scores
MCC	0.488
Average MCC ± 95% Confidence Intervals	0.428 ± 0.239
Sensitivity	0.280
Positive Predictive Value	0.855
Nr of predictions	8

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	1528	12	0	12	0	20
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...	0.50	0.25	1.00	9	12237	0	0	0	0	27
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.45	1.00	18	4735	1	0	0	1	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4JF2_A	preQ1-II links to Rfam database...	0.59	0.35	1.00	11	2839	0	0	0	0	20

Total Scores
MCC	0.253
Average MCC ± 95% Confidence Intervals	0.295 ± 0.192
Sensitivity	0.276
Positive Predictive Value	0.241
Nr of predictions	8

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_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

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