CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	Contrafold		Afold
MCC	0.567	>	0.491
Average MCC ± 95% Confidence Intervals	0.716 ± 0.056	>	0.691 ± 0.063
Sensitivity	0.505	>	0.446
Positive Predictive Value	0.637	>	0.541
Total TP	2785	>	2456
Total TN	13340831	>	13340664
Total FP	1767	<	2264
Total FP CONTRA	299	<	310
Total FP INCONS	1290	<	1775
Total FP COMP	178	<	179
Total FN	2725	<	3054
P-value	3.56938820447e-08

^top

Performance plots

^top

Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	2785
Total TN	13340831
Total FP	1767
Total FP CONTRA	299
Total FP INCONS	1290
Total FP COMP	178
Total FN	2725

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.716 ± 0.056
Sensitivity	0.505
Positive Predictive Value	0.637
Nr of predictions	95

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2K5Z_A	-	1.00	1.00	1.00	11	395	0	0	0	0	0
2K63_A	-	0.90	0.90	0.90	9	396	2	0	1	1	1
2K66_A	-	0.95	0.90	1.00	9	222	0	0	0	0	1
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	0.45	0.25	0.83	5	624	1	0	1	0	15
2KGP_A	-	1.00	1.00	1.00	9	291	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	1.00	1.00	1.00	13	548	0	0	0	0	0
2KU0_A	-	0.55	0.44	0.70	7	693	3	0	3	0	9
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
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	-	0.75	0.74	0.78	14	1467	4	2	2	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	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...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.45	0.35	0.58	7	1528	5	2	3	0	13
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
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
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	-	0.84	0.79	0.89	31	6070	6	0	4	2	8
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2WDL_A	-	0.57	0.48	0.67	582	3937349	294	33	257	4	622
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_D	-	0.39	0.23	0.67	6	1944	3	2	1	0	20
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.13	0.12	0.15	5	5117	29	1	28	0	37
2YIE_Z	-	0.43	0.42	0.45	5	1529	6	3	3	0	7
2YIE_X	-	0.73	0.67	0.80	8	1368	3	1	1	1	4
2ZY6_A	-	0.58	0.58	0.58	7	691	5	0	5	0	5
2ZZM_B	tRNA links to Rfam database...	0.53	0.47	0.60	15	3461	10	2	8	0	17
2ZZN_D	tRNA links to Rfam database...	0.82	0.78	0.88	21	2461	3	0	3	0	6
3A2K_C	tRNA links to Rfam database...	0.44	0.43	0.46	12	2900	14	2	12	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	0	9
3ADB_C	-	0.92	0.84	1.00	32	4154	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.39	0.39	0.41	11	2674	17	4	12	1	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
3DW4_A	-	-0.02	0.00	0.00	0	345	6	0	6	0	10
3G4S_9	5S_rRNA links to Rfam database...	0.30	0.25	0.38	14	7344	23	1	22	0	43
3GCA_A	-	0.49	0.29	0.83	5	522	1	0	1	0	12
3HAY_E	-	0.91	0.83	1.00	15	2263	6	0	0	6	3
3HJW_D	-	0.94	0.89	1.00	16	1637	2	0	0	2	2
3IAB_R	-	0.86	0.86	0.86	12	1021	4	1	1	2	2
3ID5_D	-	0.49	0.33	0.75	3	492	6	0	1	5	6
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.80	0.67	0.96	22	4255	1	0	1	0	11
3IYQ_A	tmRNA links to Rfam database...	0.34	0.37	0.32	35	60615	80	21	55	4	59
3IZ4_A	tmRNA links to Rfam database...	0.52	0.45	0.61	60	70777	44	4	35	5	72
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J0L_1	-	0.73	0.58	0.92	11	1213	2	0	1	1	8
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J0L_h	-	0.75	0.65	0.88	28	6073	6	0	4	2	15
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.28	0.30	0.27	8	6298	23	8	14	1	19
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.20	7	12211	35	6	22	7	26
3JYX_5	-	0.36	0.35	0.37	311	5022016	626	153	385	88	582
3KIY_A	-	0.56	0.47	0.67	585	4053253	305	29	261	15	656
3KTW_C	-	0.44	0.40	0.50	17	4526	18	2	15	1	26
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.72	0.92	44	9132	5	0	4	1	17
3NKB_B	-	0.54	0.50	0.59	13	1994	9	0	9	0	13
3NMU_E	-	0.71	0.50	1.00	3	558	3	0	0	3	3
3NPB_A	SAM links to Rfam database...	0.76	0.70	0.84	32	6983	8	1	5	2	14
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.26	0.31	9	12374	20	3	17	0	26
3O58_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	10	2	5	3	9
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	1	0	0	1	1
3R4F_A	-	0.79	0.76	0.83	19	2122	4	1	3	0	6
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SIU_F	-	0.74	0.64	0.88	7	370	1	0	1	0	4
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.59	0.46	0.77	17	3138	5	0	5	0	20
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8

^top

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	2456
Total TN	13340664
Total FP	2264
Total FP CONTRA	310
Total FP INCONS	1775
Total FP COMP	179
Total FN	3054

Total Scores
MCC	0.491
Average MCC ± 95% Confidence Intervals	0.691 ± 0.063
Sensitivity	0.446
Positive Predictive Value	0.541
Nr of predictions	95

^top

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
2K5Z_A	-	1.00	1.00	1.00	11	395	0	0	0	0	0
2K63_A	-	0.95	0.90	1.00	9	397	0	0	0	0	1
2K66_A	-	0.95	0.90	1.00	9	222	0	0	0	0	1
2KD8_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KEZ_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
2KFC_A	-	-0.02	0.00	0.00	0	622	8	0	8	0	20
2KGP_A	-	1.00	1.00	1.00	9	291	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	367	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	549	0	0	0	0	1
2KU0_A	-	0.86	0.75	1.00	12	691	0	0	0	0	4
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
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_B	Gammaretro_CES links to Rfam database...	0.96	0.96	0.96	24	2120	1	0	1	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.96	0.96	0.96	23	2056	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
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
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
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
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	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.75	0.69	0.82	9	485	2	0	2	0	4
2RP0_A	-	0.58	0.42	0.83	5	345	1	0	1	0	7
2RPT_A	-	1.00	1.00	1.00	7	183	0	0	0	0	0
2WDL_A	-	0.43	0.37	0.50	447	3937333	444	31	410	3	757
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_D	-	0.18	0.15	0.24	4	1936	13	0	13	0	22
2WW9_E	-	0.47	0.29	0.80	4	556	1	0	1	0	10
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
2YIE_Z	-	-0.01	0.00	0.00	0	1525	16	3	12	1	12
2YIE_X	-	0.36	0.33	0.40	4	1368	8	2	4	2	8
2ZY6_A	-	0.55	0.58	0.54	7	690	6	1	5	0	5
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.25	6	3462	18	0	18	0	26
2ZZN_D	tRNA links to Rfam database...	0.80	0.74	0.87	20	2462	3	0	3	0	7
3A2K_C	tRNA links to Rfam database...	0.41	0.39	0.44	11	2901	14	2	12	0	17
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.70	1.00	26	3629	0	0	0	0	11
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
3DW4_A	-	-0.02	0.00	0.00	0	344	7	0	7	0	10
3G4S_9	5S_rRNA links to Rfam database...	0.48	0.35	0.67	20	7351	11	1	9	1	37
3GCA_A	-	-0.02	0.00	0.00	0	519	9	0	9	0	17
3HAY_E	-	0.91	0.83	1.00	15	2263	7	0	0	7	3
3HJW_D	-	0.91	0.89	0.94	16	1636	3	0	1	2	2
3IAB_R	-	0.92	0.86	1.00	12	1023	0	0	0	0	2
3ID5_D	-	0.40	0.33	0.50	3	490	6	0	3	3	6
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.62	0.58	0.68	19	4250	9	0	9	0	14
3IYQ_A	tmRNA links to Rfam database...	0.31	0.34	0.29	32	60616	82	23	55	4	62
3IZ4_A	tmRNA links to Rfam database...	0.48	0.45	0.51	59	70760	58	11	46	1	73
3IZF_C	5S_rRNA links to Rfam database...	0.66	0.57	0.76	31	6862	10	1	9	0	23
3J0L_1	-	0.73	0.63	0.86	12	1211	3	0	2	1	7
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
3J0L_h	-	0.73	0.60	0.90	26	6076	5	0	3	2	17
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2827	23	1	22	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.54	0.56	0.54	15	6300	24	1	12	11	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	35	5	17	13	23
3JYX_5	-	0.29	0.30	0.29	268	5021928	735	179	490	66	625
3KIY_A	-	0.43	0.36	0.50	449	4053235	456	24	420	12	792
3KTW_C	-	0.71	0.63	0.82	27	4527	7	2	4	1	16
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
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
3NPB_A	SAM links to Rfam database...	0.74	0.61	0.90	28	6990	5	0	3	2	18
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	23
3O58_2	5S_rRNA links to Rfam database...	0.66	0.66	0.66	25	7222	14	4	9	1	13
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
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

^top

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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

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

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

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