CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Afold		UNAFold
MCC	0.493	>	0.485
Average MCC ± 95% Confidence Intervals	0.559 ± 0.134	<	0.595 ± 0.132
Sensitivity	0.537	>	0.524
Positive Predictive Value	0.453	>	0.450
Total TP	1397	>	1363
Total TN	4970891	<	4970947
Total FP	2083	>	2054
Total FP CONTRA	525	>	505
Total FP INCONS	1163	>	1161
Total FP COMP	395	>	388
Total FN	1206	<	1240
P-value	5.12827206146e-07

Comparison of performance of Afold and UNAFold. 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 Afold and UNAFold).
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 Afold and UNAFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and UNAFold. 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 Afold and UNAFold).

Total Scores
MCC	0.493
Average MCC ± 95% Confidence Intervals	0.559 ± 0.134
Sensitivity	0.537
Positive Predictive Value	0.453
Nr of predictions	24

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	228	8	1	7	0	8
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
2RP0_A	-	0.76	0.71	0.83	5	110	1	0	1	0	2
2WDL_A	-	0.52	0.54	0.50	426	1444477	465	78	341	46	362
2ZZN_D	tRNA links to Rfam database...	0.91	0.91	0.91	20	962	3	2	0	1	2
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3GCA_A	-	-0.04	0.00	0.00	0	151	9	1	6	2	7
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.67	0.68	0.68	19	1444	9	1	8	0	9
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3JYX_5	-	0.34	0.44	0.27	210	1968232	793	260	300	233	271
3KIY_A	-	0.53	0.55	0.51	430	1485031	475	81	338	56	356
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

Total Scores
MCC	0.485
Average MCC ± 95% Confidence Intervals	0.595 ± 0.132
Sensitivity	0.524
Positive Predictive Value	0.450
Nr of predictions	24

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	-0.03	0.00	0.00	0	229	7	1	6	0	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2WDL_A	-	0.49	0.50	0.47	396	1444479	488	87	360	41	392
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.79	0.81	22	1445	6	1	4	1	6
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	96	46	38	12	34
3IZ4_A	tmRNA links to Rfam database...	0.58	0.60	0.57	57	25436	53	12	31	10	38
3JYV_7	tRNA links to Rfam database...	0.24	0.25	0.25	5	1091	16	7	8	1	15
3JYX_5	-	0.36	0.45	0.29	216	1968262	763	245	279	239	265
3KIY_A	-	0.50	0.52	0.48	410	1485034	486	79	357	50	376
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NPB_A	SAM links to Rfam database...	0.85	0.78	0.94	29	2247	6	0	2	4	8
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	34	5	15	14	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	11	17	14	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4

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