CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		NanoFolder
MCC	0.638	>	0.412
Average MCC ± 95% Confidence Intervals	0.556 ± 0.257	>	0.427 ± 0.199
Sensitivity	0.417	<	0.506
Positive Predictive Value	0.985	>	0.350
Total TP	65	<	79
Total TN	12126	>	11966
Total FP	7	<	169
Total FP CONTRA	1	<	52
Total FP INCONS	0	<	95
Total FP COMP	6	<	22
Total FN	91	>	77
P-value	0.0

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

Total Scores
MCC	0.638
Average MCC ± 95% Confidence Intervals	0.556 ± 0.257
Sensitivity	0.417
Positive Predictive Value	0.985
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...	0.00	0.00	0.00	0	528	0	0	0	0	18
3J16_L	tRNA links to Rfam database...	0.53	0.29	1.00	6	1153	0	0	0	0	15
3UZL_B	tRNA links to Rfam database...	0.50	0.25	1.00	4	1289	2	0	0	2	12
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.43	1.00	16	2747	0	0	0	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7

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

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