CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		NanoFolder
MCC	0.621	>	0.438
Average MCC ± 95% Confidence Intervals	0.727 ± 0.121	>	0.616 ± 0.151
Sensitivity	0.620	>	0.529
Positive Predictive Value	0.633	>	0.378
Total TP	245	>	209
Total TN	26924	>	26758
Total FP	163	<	371
Total FP CONTRA	41	<	117
Total FP INCONS	101	<	227
Total FP COMP	21	<	27
Total FN	150	<	186
P-value	5.1503931209e-08

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

Total Scores
MCC	0.621
Average MCC ± 95% Confidence Intervals	0.727 ± 0.121
Sensitivity	0.620
Positive Predictive Value	0.633
Nr of predictions	21

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...	0.64	0.61	0.69	11	512	5	1	4	0	7
2LDL_A	-	0.81	0.67	1.00	6	134	0	0	0	0	3
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	-	0.56	0.55	0.57	16	2412	13	4	8	1	13
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...	0.71	0.75	0.68	15	1090	8	2	5	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	11
3SN2_B	IRE_II links to Rfam database...	0.63	0.42	1.00	5	149	0	0	0	0	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3UZL_B	tRNA links to Rfam database...	0.45	0.50	0.42	8	1274	18	4	7	7	8
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
3W3S_B	tRNA-Sec links to Rfam database...	0.48	0.45	0.52	15	1960	15	1	13	1	18
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.69	0.71	24	2762	11	5	5	1	11
3ZEX_E	-	0.00	0.00	0.00	0	8258	51	15	31	5	34
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ATO_G	-	0.88	1.00	0.78	7	211	2	2	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4HXH_A	-	1.00	1.00	1.00	6	89	0	0	0	0	0

Total Scores
MCC	0.438
Average MCC ± 95% Confidence Intervals	0.616 ± 0.151
Sensitivity	0.529
Positive Predictive Value	0.378
Nr of predictions	21

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
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_E	-	0.03	0.06	0.02	2	8222	86	31	49	6	32
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
4ATO_G	-	0.72	1.00	0.54	7	207	6	6	0	0	0
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.