CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Afold		Cylofold
MCC	0.712	>	0.669
Average MCC ± 95% Confidence Intervals	0.726 ± 0.089	>	0.701 ± 0.080
Sensitivity	0.655	>	0.582
Positive Predictive Value	0.780	>	0.775
Total TP	646	>	574
Total TN	98452	<	98539
Total FP	213	>	184
Total FP CONTRA	18	>	15
Total FP INCONS	164	>	152
Total FP COMP	31	>	17
Total FN	340	<	412
P-value	3.56938820447e-08

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Performance plots

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Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	646
Total TN	98452
Total FP	213
Total FP CONTRA	18
Total FP INCONS	164
Total FP COMP	31
Total FN	340

Total Scores
MCC	0.712
Average MCC ± 95% Confidence Intervals	0.726 ± 0.089
Sensitivity	0.655
Positive Predictive Value	0.780
Nr of predictions	43

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2. Individual counts for Afold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.89	0.80	1.00	8	343	0	0	0	0	2
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_A	Gammaretro_CES links to Rfam database...	0.96	0.96	0.96	23	2056	1	0	1	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.96	0.96	24	2120	1	0	1	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2LWK_A	-	0.75	0.69	0.82	9	485	2	0	2	0	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
2YIE_X	-	0.36	0.33	0.40	4	1368	8	2	4	2	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	16	3	12	1	12
3ADB_C	-	0.78	0.74	0.82	28	4152	6	0	6	0	10
3AKZ_H	tRNA links to Rfam database...	0.16	0.14	0.19	4	2680	17	2	15	0	24
3AM1_B	-	0.72	0.66	0.79	23	3211	6	0	6	0	12
3IZF_C	5S_rRNA links to Rfam database...	0.66	0.57	0.76	31	6862	10	1	9	0	23
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
3J0L_1	-	0.73	0.63	0.86	12	1211	3	0	2	1	7
3J0L_h	-	0.73	0.60	0.90	26	6076	5	0	3	2	17
3NDB_M	-	0.84	0.74	0.96	45	9133	3	0	2	1	16
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	553	10	1	7	2	6
3O58_2	5S_rRNA links to Rfam database...	0.66	0.66	0.66	25	7222	14	4	9	1	13
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	23
3OVS_D	-	0.80	0.77	0.83	10	549	2	0	2	0	3
3P22_G	-	0.87	0.83	0.91	10	730	1	0	1	0	2
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	1	0	0	1	1
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

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Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	574
Total TN	98539
Total FP	184
Total FP CONTRA	15
Total FP INCONS	152
Total FP COMP	17
Total FN	412

Total Scores
MCC	0.669
Average MCC ± 95% Confidence Intervals	0.701 ± 0.080
Sensitivity	0.582
Positive Predictive Value	0.775
Nr of predictions	43

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2. Individual counts for Cylofold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.70	0.50	1.00	5	346	0	0	0	0	5
2KZL_A	-	0.72	0.53	1.00	10	1475	0	0	0	0	9
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.83	1.00	20	2060	0	0	0	0	4
2L1F_B	Gammaretro_CES links to Rfam database...	0.92	0.84	1.00	21	2124	0	0	0	0	4
2L2K_A	-	0.82	0.68	1.00	13	848	0	0	0	0	6
2L3C_B	-	0.76	0.59	1.00	10	551	0	0	0	0	7
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.89	0.79	1.00	27	2458	0	0	0	0	7
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
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
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
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
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.10	0.11	4	5115	32	1	31	0	38
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
3ADB_C	-	0.78	0.71	0.87	27	4155	4	0	4	0	11
3AKZ_H	tRNA links to Rfam database...	0.66	0.57	0.76	16	2680	6	0	5	1	12
3AM1_B	-	0.76	0.63	0.92	22	3216	2	0	2	0	13
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
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
3NDB_M	-	0.58	0.48	0.71	29	9139	13	1	11	1	32
3NKB_B	-	0.40	0.31	0.53	8	2001	7	0	7	0	18
3NMU_E	-	0.20	0.17	0.25	1	557	6	1	2	3	5
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3OVS_D	-	0.96	0.92	1.00	12	549	0	0	0	0	1
3P22_G	-	0.96	0.92	1.00	11	730	0	0	0	0	1
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
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
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
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
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4

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

Table of contents:

Overview

Performance plots

Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

2. Individual counts for Afold [ download as .csv ]

Performance of Cylofold - scored lower in this pairwise comparison

1. Total counts & total scores for Cylofold

2. Individual counts for Cylofold [ download as .csv ]