CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CentroidHomfold‑LAST		Cylofold
MCC	0.663	>	0.586
Average MCC ± 95% Confidence Intervals	0.656 ± 0.101	>	0.615 ± 0.096
Sensitivity	0.487	<	0.499
Positive Predictive Value	0.909	>	0.698
Total TP	339	<	347
Total TN	61165	>	61041
Total FP	46	<	162
Total FP CONTRA	0	<	16
Total FP INCONS	34	<	134
Total FP COMP	12	=	12
Total FN	357	>	349
P-value	3.56938820447e-08

Total Scores
MCC	0.663
Average MCC ± 95% Confidence Intervals	0.656 ± 0.101
Sensitivity	0.487
Positive Predictive Value	0.909
Nr of predictions	35

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
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
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.72	0.53	1.00	8	457	0	0	0	0	7
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.00	0.00	0.00	0	6101	4	0	4	0	39
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2Y9C_V	-	0.20	0.04	1.00	1	2277	0	0	0	0	23
2YIE_X	-	0.76	0.58	1.00	7	1371	0	0	0	0	5
2YIE_Z	-	0.82	0.67	1.00	8	1532	0	0	0	0	4
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_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_h	-	0.76	0.63	0.93	27	6076	4	0	2	2	16
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_2	-	0.49	0.24	1.00	8	6208	0	0	0	0	25
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3NMU_E	-	0.41	0.17	1.00	1	560	3	0	0	3	5
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
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
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
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
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
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

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.615 ± 0.096
Sensitivity	0.499
Positive Predictive Value	0.698
Nr of predictions	35

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
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
2LDL_A	-	0.73	0.55	1.00	6	345	0	0	0	0	5
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
2LWK_A	-	0.83	0.77	0.91	10	485	1	0	1	0	3
2RRC_A	-	0.70	0.50	1.00	5	226	0	0	0	0	5
2Y9C_V	-	0.59	0.54	0.65	13	2258	8	1	6	1	11
2YIE_X	-	0.30	0.33	0.29	4	1364	10	2	8	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1529	11	3	8	0	12
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_1	-	0.65	0.47	0.90	9	1215	2	0	1	1	10
3J0L_h	-	0.48	0.37	0.62	16	6079	10	0	10	0	27
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3NMU_E	-	0.20	0.17	0.25	1	557	6	1	2	3	5
3R9X_C	-	0.84	0.80	0.89	8	586	2	0	1	1	2
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
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	0.64	0.42	1.00	5	401	0	0	0	0	7
3TRZ_Z	-	0.91	0.83	1.00	5	205	1	0	0	1	1
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
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
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
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

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