CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MCFold		NanoFolder
MCC	0.636	>	0.522
Average MCC ± 95% Confidence Intervals	0.718 ± 0.164	>	0.684 ± 0.170
Sensitivity	0.654	>	0.538
Positive Predictive Value	0.624	>	0.515
Total TP	214	>	176
Total TN	36721	<	36722
Total FP	166	<	177
Total FP CONTRA	15	<	27
Total FP INCONS	114	<	139
Total FP COMP	37	>	11
Total FN	113	<	151
P-value	1.45096400029e-08

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

Total Scores
MCC	0.636
Average MCC ± 95% Confidence Intervals	0.718 ± 0.164
Sensitivity	0.654
Positive Predictive Value	0.624
Nr of predictions	15

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...	0.41	0.45	0.39	9	1517	16	0	14	2	11
2LDL_A	-	0.95	0.91	1.00	10	341	2	0	0	2	1
2LI4_A	-	0.97	0.94	1.00	15	481	0	0	0	0	1
2LK3_A	-	1.00	1.00	1.00	10	266	0	0	0	0	0
2LKR_A	-	0.93	0.92	0.95	36	6067	14	0	2	12	3
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.92	0.92	0.92	12	483	2	0	1	1	1
3J16_L	tRNA links to Rfam database...	0.45	0.47	0.44	14	2743	19	1	17	1	16
3SN2_B	IRE_II links to Rfam database...	0.55	0.58	0.54	7	393	6	0	6	0	5
3U4M_B	-	0.59	0.59	0.59	22	3123	15	0	15	0	15
3VJR_D	-	1.00	1.00	1.00	13	617	1	0	0	1	0
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.67	0.71	36	7089	17	1	14	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.11	5	11735	56	10	31	15	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.28	0.32	0.27	6	1304	17	2	14	1	13

Total Scores
MCC	0.522
Average MCC ± 95% Confidence Intervals	0.684 ± 0.170
Sensitivity	0.538
Positive Predictive Value	0.515
Nr of predictions	15

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
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
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
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
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.