CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		NanoFolder
MCC	0.752	>	0.374
Average MCC ± 95% Confidence Intervals	0.778 ± 0.151	>	0.558 ± 0.155
Sensitivity	0.698	>	0.463
Positive Predictive Value	0.816	>	0.317
Total TP	338	>	224
Total TN	40406	>	40114
Total FP	128	<	530
Total FP CONTRA	17	<	156
Total FP INCONS	59	<	326
Total FP COMP	52	>	48
Total FN	146	<	260
P-value	5.1503931209e-08

Comparison of performance of CentroidHomfold-LAST 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 CentroidHomfold‑LAST 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 CentroidHomfold‑LAST and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST 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 CentroidHomfold‑LAST and NanoFolder).

Total Scores
MCC	0.752
Average MCC ± 95% Confidence Intervals	0.778 ± 0.151
Sensitivity	0.698
Positive Predictive Value	0.816
Nr of predictions	23

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	517	11	0	11	0	18
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.00	0.00	0.00	0	2436	4	0	4	0	29
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2986	8	0	2	6	2
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	144	0	0	0	0	2
3U4M_B	-	0.78	0.73	0.84	16	1257	4	0	3	1	6
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.88	1.00	29	1960	1	0	0	1	4
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.83	0.91	29	2764	8	0	3	5	6
3ZEX_G	-	0.97	0.93	1.00	42	6465	10	0	0	10	3
3ZEX_E	-	0.00	0.00	0.00	0	8273	33	9	22	2	34
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	7	0	6	1	8
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

Total Scores
MCC	0.374
Average MCC ± 95% Confidence Intervals	0.558 ± 0.155
Sensitivity	0.463
Positive Predictive Value	0.317
Nr of predictions	23

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
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
2LWK_A	-	0.95	0.91	1.00	10	197	2	0	0	2	1
3J16_L	tRNA links to Rfam database...	0.43	0.52	0.37	11	1129	19	8	11	0	10
3J20_1	tRNA links to Rfam database...	0.42	0.50	0.37	10	1085	20	5	12	3	10
3J2L_3	5S_rRNA links to Rfam database...	0.13	0.18	0.12	6	2969	46	14	31	1	28
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
3UZL_B	tRNA links to Rfam database...	0.41	0.56	0.31	9	1264	25	10	10	5	7
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.18	0.21	0.18	7	1949	34	2	31	1	26
3ZEX_D	5S_rRNA links to Rfam database...	0.30	0.37	0.27	13	2747	36	10	26	0	22
3ZEX_G	-	0.04	0.07	0.04	3	6431	77	18	55	4	42
3ZEX_E	-	0.03	0.06	0.02	2	8222	86	31	49	6	32
4A1C_2	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	4469	61	18	29	14	20
4A1C_3	5S_rRNA links to Rfam database...	0.58	0.68	0.51	25	2714	24	9	15	0	12
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
4HXH_A	-	0.80	1.00	0.67	6	86	3	3	0	0	0

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