CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		McQFold
MCC	0.699	>	0.578
Average MCC ± 95% Confidence Intervals	0.733 ± 0.103	>	0.676 ± 0.123
Sensitivity	0.586	>	0.505
Positive Predictive Value	0.838	>	0.670
Total TP	346	>	298
Total TN	63681	>	63649
Total FP	90	<	163
Total FP CONTRA	6	<	13
Total FP INCONS	61	<	134
Total FP COMP	23	>	16
Total FN	244	<	292
P-value	5.23657817852e-08

Total Scores
MCC	0.699
Average MCC ± 95% Confidence Intervals	0.733 ± 0.103
Sensitivity	0.586
Positive Predictive Value	0.838
Nr of predictions	29

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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LJJ_A	-	0.93	0.88	1.00	7	344	2	0	0	2	1
2LK3_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2LKR_A	-	0.65	0.56	0.76	22	6076	9	0	7	2	17
2LQZ_A	-	0.80	0.73	0.89	8	342	1	1	0	0	3
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
3J0L_2	-	0.64	0.61	0.69	20	6187	11	2	7	2	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_h	-	0.82	0.67	1.00	29	6076	2	0	0	2	14
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J0L_1	-	0.70	0.58	0.85	11	1212	3	0	2	1	8
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
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
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.578
Average MCC ± 95% Confidence Intervals	0.676 ± 0.123
Sensitivity	0.505
Positive Predictive Value	0.670
Nr of predictions	29

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...	0.61	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
2LHP_A	-	1.00	1.00	1.00	16	650	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.51	0.46	0.58	18	6074	13	2	11	0	21
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
3J0L_2	-	0.26	0.24	0.30	8	6189	21	0	19	2	25
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_h	-	0.65	0.49	0.88	21	6081	3	0	3	0	22
3J0L_7	-	-0.01	0.00	0.00	0	1215	10	0	10	0	17
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_1	-	0.65	0.47	0.90	9	1215	3	0	1	2	10
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3U4M_B	-	0.73	0.57	0.95	21	3138	1	0	1	0	16
3UZL_B	tRNA links to Rfam database...	0.45	0.41	0.52	15	3541	14	0	14	0	22
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_3	5S_rRNA links to Rfam database...	0.25	0.22	0.29	12	7099	29	1	28	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	33	5	23	5	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
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.