CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAshapes		NanoFolder
MCC	0.514	>	0.366
Average MCC ± 95% Confidence Intervals	0.496 ± 0.175	>	0.390 ± 0.143
Sensitivity	0.447	>	0.376
Positive Predictive Value	0.599	>	0.364
Total TP	139	>	117
Total TN	41536	>	41447
Total FP	106	<	214
Total FP CONTRA	11	<	30
Total FP INCONS	82	<	174
Total FP COMP	13	>	10
Total FN	172	<	194
P-value	0.0

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

Total Scores
MCC	0.514
Average MCC ± 95% Confidence Intervals	0.496 ± 0.175
Sensitivity	0.447
Positive Predictive Value	0.599
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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.93	0.87	1.00	34	6071	1	0	0	1	5
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.39	0.32	0.48	12	3545	13	2	11	0	25
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.57	0.82	31	7102	7	1	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11746	41	5	25	11	28
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	1	6	0	14

Total Scores
MCC	0.366
Average MCC ± 95% Confidence Intervals	0.390 ± 0.143
Sensitivity	0.376
Positive Predictive Value	0.364
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
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
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

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