CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		Afold
MCC	0.690	>	0.590
Average MCC ± 95% Confidence Intervals	0.806 ± 0.057	>	0.767 ± 0.066
Sensitivity	0.715	>	0.630
Positive Predictive Value	0.666	>	0.553
Total TP	2614	>	2303
Total TN	5020966	>	5020728
Total FP	1938	<	2417
Total FP CONTRA	476	<	566
Total FP INCONS	834	<	1293
Total FP COMP	628	>	558
Total FN	1040	<	1351
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Contrafold and Afold. 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 Contrafold and Afold).
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 Contrafold and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Contrafold and Afold. 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 Contrafold and Afold).

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Performance of Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	2614
Total TN	5020966
Total FP	1938
Total FP CONTRA	476
Total FP INCONS	834
Total FP COMP	628
Total FN	1040

Total Scores
MCC	0.690
Average MCC ± 95% Confidence Intervals	0.806 ± 0.057
Sensitivity	0.715
Positive Predictive Value	0.666
Nr of predictions	95

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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	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	2	0	0	2	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	0.71	0.63	0.83	5	230	1	1	0	0	3
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	1.00	1.00	1.00	13	200	0	0	0	0	0
2KU0_A	-	0.63	0.58	0.70	7	282	3	2	1	0	5
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	1.00	1.00	1.00	8	141	0	0	0	0	0
2KZL_A	-	1.00	1.00	1.00	13	507	5	0	0	5	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.39	0.58	7	516	5	3	2	0	11
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.88	0.90	0.87	26	2410	11	0	4	7	3
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2WDL_A	-	0.69	0.71	0.68	556	1444510	320	75	181	64	232
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_D	-	0.63	0.40	1.00	4	737	5	0	0	5	6
2WW9_E	-	0.00	0.00	0.00	0	172	0	0	0	0	5
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.12	4	2012	30	2	27	1	31
2YIE_Z	-	0.53	0.63	0.45	5	591	6	4	2	0	3
2YIE_X	-	1.00	1.00	1.00	7	537	4	0	0	4	0
2ZY6_A	-	0.69	0.78	0.64	7	265	5	2	2	1	2
2ZZM_B	tRNA links to Rfam database...	0.80	0.80	0.80	12	1343	13	0	3	10	3
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	3	2	0	1	1
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3ADB_C	-	0.98	0.97	1.00	32	1787	0	0	0	0	1
3AKZ_H	tRNA links to Rfam database...	0.44	0.50	0.40	10	1102	18	6	9	3	10
3AM1_B	-	0.74	0.76	0.73	22	1436	8	3	5	0	7
3DW4_A	-	-0.03	0.00	0.00	0	136	6	1	3	2	6
3G4S_9	5S_rRNA links to Rfam database...	0.45	0.50	0.42	13	2705	24	6	12	6	13
3GCA_A	-	0.76	0.71	0.83	5	152	1	1	0	0	2
3HAY_E	-	1.00	1.00	1.00	14	910	7	0	0	7	0
3HJW_D	-	1.00	1.00	1.00	16	593	2	0	0	2	0
3IAB_R	-	1.00	1.00	1.00	12	373	4	0	0	4	0
3ID5_D	-	0.66	0.60	0.75	3	225	6	0	1	5	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.86	0.79	0.96	22	1449	1	0	1	0	6
3IYQ_A	tmRNA links to Rfam database...	0.28	0.39	0.20	20	22341	95	44	35	16	31
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.57	55	25440	49	18	23	8	40
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3J0L_1	-	0.83	0.77	0.91	10	473	3	0	1	2	3
3J0L_7	-	-0.02	0.00	0.00	0	512	7	1	6	0	10
3J0L_h	-	0.87	0.88	0.88	28	2108	6	0	4	2	4
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.33	0.47	0.24	7	2349	24	16	6	2	8
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.58	0.27	7	4730	35	13	6	16	5
3JYX_5	-	0.43	0.50	0.37	240	1968358	697	172	232	293	241
3KIY_A	-	0.70	0.71	0.69	561	1485072	329	73	174	82	225
3KTW_C	-	0.56	0.60	0.54	15	1752	20	2	11	7	10
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	0.98	0.98	0.98	43	3670	6	0	1	5	1
3NKB_B	-	0.63	0.68	0.59	13	713	9	0	9	0	6
3NMU_E	-	1.00	1.00	1.00	3	213	3	0	0	3	0
3NPB_A	SAM links to Rfam database...	0.86	0.84	0.89	31	2243	9	1	3	5	6
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.36	0.29	8	4736	21	7	13	1	14
3O58_2	5S_rRNA links to Rfam database...	0.92	0.94	0.91	29	2722	10	0	3	7	2
3OVS_D	-	1.00	1.00	1.00	12	204	0	0	0	0	0
3P22_G	-	1.00	1.00	1.00	11	301	1	0	0	1	0
3R4F_A	-	0.81	0.82	0.82	18	884	5	2	2	1	4
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SIU_F	-	0.87	0.88	0.88	7	137	1	0	1	0	1
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.81	0.77	0.85	17	1256	5	0	3	2	5
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	33	9	13	11	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4

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Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	2303
Total TN	5020728
Total FP	2417
Total FP CONTRA	566
Total FP INCONS	1293
Total FP COMP	558
Total FN	1351

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.767 ± 0.066
Sensitivity	0.630
Positive Predictive Value	0.553
Nr of predictions	95

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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
2K5Z_A	-	1.00	1.00	1.00	11	175	0	0	0	0	0
2K63_A	-	1.00	1.00	1.00	9	159	0	0	0	0	0
2K66_A	-	1.00	1.00	1.00	9	80	0	0	0	0	0
2KD8_A	-	1.00	1.00	1.00	9	99	0	0	0	0	0
2KDQ_B	mir-TAR links to Rfam database...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	0
2KEZ_A	-	1.00	1.00	1.00	8	94	0	0	0	0	0
2KFC_A	-	-0.03	0.00	0.00	0	228	8	1	7	0	8
2KGP_A	-	1.00	1.00	1.00	9	112	1	0	0	1	0
2KMJ_A	-	1.00	1.00	1.00	11	157	0	0	0	0	0
2KPV_A	-	0.96	0.92	1.00	12	201	0	0	0	0	1
2KU0_A	-	1.00	1.00	1.00	12	280	0	0	0	0	0
2KUR_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	448	0	0	0	0	0
2KUU_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	429	1	0	0	1	0
2KUV_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	19	420	0	0	0	0	0
2KUW_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	452	1	0	0	1	0
2KX8_A	7SK links to Rfam database...	1.00	1.00	1.00	16	355	0	0	0	0	0
2KXM_A	-	1.00	1.00	1.00	8	141	0	0	0	0	0
2KZL_A	-	1.00	1.00	1.00	13	507	1	0	0	1	0
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	24	766	1	0	1	0	0
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	1.00	0.96	23	739	1	0	1	0	0
2L2K_A	-	1.00	1.00	1.00	17	332	0	0	0	0	0
2L3C_B	-	1.00	1.00	1.00	14	225	0	0	0	0	0
2L3E_A	-	1.00	1.00	1.00	12	228	1	0	0	1	0
2L3J_B	mir-2985-2 links to Rfam database...	1.00	1.00	1.00	30	955	0	0	0	0	0
2L5Z_A	-	1.00	1.00	1.00	9	102	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	6	0	5	1	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.85	0.82	0.90	9	197	2	0	1	1	2
2RP0_A	-	0.76	0.71	0.83	5	110	1	0	1	0	2
2RPT_A	-	1.00	1.00	1.00	7	65	0	0	0	0	0
2WDL_A	-	0.52	0.54	0.50	426	1444477	465	78	341	46	362
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	14	0	0	14	0
2WW9_F	-	0.68	0.75	0.67	6	103	4	1	2	1	2
2WW9_D	-	0.08	0.10	0.08	1	729	16	2	9	5	9
2WW9_E	-	0.79	0.80	0.80	4	167	1	0	1	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.38	12	2013	21	1	19	1	23
2YIE_Z	-	-0.02	0.00	0.00	0	587	16	6	9	1	8
2YIE_X	-	0.53	0.57	0.50	4	536	8	1	3	4	3
2ZY6_A	-	0.63	0.78	0.54	7	263	6	3	3	0	2
2ZZM_B	tRNA links to Rfam database...	0.25	0.27	0.25	4	1342	20	3	9	8	11
2ZZN_D	tRNA links to Rfam database...	0.91	0.91	0.91	20	962	3	2	0	1	2
3A2K_C	tRNA links to Rfam database...	0.46	0.50	0.44	11	1083	14	3	11	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.93	0.87	1.00	26	1474	0	0	0	0	4
3ADB_C	-	0.85	0.85	0.85	28	1786	6	0	5	1	5
3AKZ_H	tRNA links to Rfam database...	0.19	0.20	0.21	4	1108	17	4	11	2	16
3AM1_B	-	0.79	0.79	0.79	23	1437	6	0	6	0	6
3DW4_A	-	-0.04	0.00	0.00	0	135	7	1	4	2	6
3G4S_9	5S_rRNA links to Rfam database...	0.73	0.69	0.78	18	2713	13	2	3	8	8
3GCA_A	-	-0.04	0.00	0.00	0	151	9	1	6	2	7
3HAY_E	-	1.00	1.00	1.00	14	910	8	0	0	8	0
3HJW_D	-	0.97	1.00	0.94	16	592	3	0	1	2	0
3IAB_R	-	1.00	1.00	1.00	12	373	0	0	0	0	0
3ID5_D	-	0.59	0.60	0.60	3	224	6	0	2	4	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	0.67	0.68	0.68	19	1444	9	1	8	0	9
3IYQ_A	tmRNA links to Rfam database...	0.23	0.33	0.17	17	22339	97	47	37	13	34
3IZ4_A	tmRNA links to Rfam database...	0.52	0.57	0.48	54	25423	63	27	32	4	41
3IZF_C	5S_rRNA links to Rfam database...	0.83	0.86	0.81	30	2603	11	0	7	4	5
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_7	-	-0.02	0.00	0.00	0	504	15	1	14	0	10
3J0L_h	-	0.87	0.81	0.93	26	2112	5	1	1	3	6
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1088	23	4	19	0	20
3JYX_3	5S_rRNA links to Rfam database...	0.64	0.67	0.63	10	2362	29	0	6	23	5
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3JYX_5	-	0.34	0.44	0.27	210	1968232	793	260	300	233	271
3KIY_A	-	0.53	0.55	0.51	430	1485031	475	81	338	56	356
3KTW_C	-	0.94	0.96	0.92	24	1754	10	0	2	8	1
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NDB_M	-	1.00	1.00	1.00	44	3670	4	0	0	4	0
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3NMU_E	-	-0.02	0.00	0.00	0	208	10	5	3	2	3
3NPB_A	SAM links to Rfam database...	0.82	0.73	0.93	27	2249	6	0	2	4	10
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3O58_2	5S_rRNA links to Rfam database...	0.80	0.81	0.81	25	2723	14	0	6	8	6
3OVS_D	-	0.82	0.83	0.83	10	204	2	0	2	0	2
3P22_G	-	0.91	0.91	0.91	10	301	1	0	1	0	1
3R4F_A	-	1.00	1.00	1.00	22	884	1	0	0	1	0
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SIU_F	-	1.00	1.00	1.00	8	137	0	0	0	0	0
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	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 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 ]