CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidHomfold‑LAST		Cylofold
MCC	0.512	>	0.483
Average MCC ± 95% Confidence Intervals	0.476 ± 0.128	<	0.499 ± 0.093
Sensitivity	0.380	<	0.401
Positive Predictive Value	0.696	>	0.590
Total TP	334	<	352
Total TN	113395	>	113278
Total FP	158	<	260
Total FP CONTRA	10	<	19
Total FP INCONS	136	<	226
Total FP COMP	12	<	15
Total FN	544	>	526
P-value	5.19332990918e-08

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

Total Scores
MCC	0.512
Average MCC ± 95% Confidence Intervals	0.476 ± 0.128
Sensitivity	0.380
Positive Predictive Value	0.696
Nr of predictions	27

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1529	11	0	11	0	20
2LKR_A	-	0.00	0.00	0.00	0	6101	4	0	4	0	39
2M58_A	-	-0.01	0.00	0.00	0	1648	5	0	5	0	17
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J0L_2	-	0.49	0.24	1.00	8	6208	0	0	0	0	25
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.35	0.37	0.34	11	2818	22	3	18	1	19
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J2C_O	-	0.00	0.00	0.00	0	10296	0	0	0	0	63
3J2L_3	5S_rRNA links to Rfam database...	0.73	0.62	0.87	33	7837	7	0	5	2	20
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.64	0.45	0.90	19	3895	2	0	2	0	23
3U4M_B	-	0.58	0.43	0.80	16	3140	4	0	4	0	21
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	29	4724	1	0	0	1	11
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	0	5	0	17
3ZEX_E	-	0.00	0.00	0.00	0	21914	33	1	30	2	77
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.41	0.41	0.43	13	3456	17	3	14	0	19
4FRN_A	AdoCbl-variant links to Rfam database...	0.36	0.39	0.34	14	5110	27	3	24	0	22

Total Scores
MCC	0.483
Average MCC ± 95% Confidence Intervals	0.499 ± 0.093
Sensitivity	0.401
Positive Predictive Value	0.590
Nr of predictions	27

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
2M58_A	-	0.51	0.41	0.64	7	1642	4	1	3	0	10
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_1	tRNA links to Rfam database...	0.69	0.70	0.70	16	2903	7	2	5	0	7
3J2C_O	-	0.43	0.33	0.55	21	10258	18	0	17	1	42
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.52	15	4724	15	0	14	1	25
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.49	0.69	24	6986	11	0	11	0	25
3ZEX_E	-	0.00	0.00	0.00	0	21897	51	2	46	3	77
3ZND_W	tRNA links to Rfam database...	0.40	0.39	0.41	9	2981	15	2	11	2	14
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.14	0.31	5	5135	11	2	9	0	31

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