CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CRWrnafold		NanoFolder
MCC	0.687	>	0.542
Average MCC ± 95% Confidence Intervals	0.752 ± 0.192	>	0.683 ± 0.191
Sensitivity	0.694	>	0.635
Positive Predictive Value	0.689	>	0.478
Total TP	175	>	160
Total TN	15181	>	15100
Total FP	106	<	201
Total FP CONTRA	22	<	63
Total FP INCONS	57	<	112
Total FP COMP	27	>	26
Total FN	77	<	92
P-value	2.59578924681e-08

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

Total Scores
MCC	0.687
Average MCC ± 95% Confidence Intervals	0.752 ± 0.192
Sensitivity	0.694
Positive Predictive Value	0.689
Nr of predictions	14

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	0.94	0.89	1.00	8	132	1	0	0	1	1
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.58	0.55	0.62	16	2414	13	4	6	3	13
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	7	0	5	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	8	4	3	1	9
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	2	0	0	2	4

Total Scores
MCC	0.542
Average MCC ± 95% Confidence Intervals	0.683 ± 0.191
Sensitivity	0.635
Positive Predictive Value	0.478
Nr of predictions	14

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
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.26	0.34	0.21	10	2392	41	15	23	3	19
2LQZ_A	-	1.00	1.00	1.00	8	124	3	0	0	3	0
3J16_L	tRNA links to Rfam database...	0.43	0.52	0.37	11	1129	19	8	11	0	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.77	0.91	0.67	20	1246	12	6	4	2	2
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
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
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.