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		McQFold
MCC	0.500	>	0.363
Average MCC ± 95% Confidence Intervals	0.526 ± 0.056	>	0.484 ± 0.064
Sensitivity	0.437	>	0.287
Positive Predictive Value	0.573	>	0.459
Total TP	3322	>	2185
Total TN	15811989	<	15813026
Total FP	2705	>	2681
Total FP CONTRA	370	>	220
Total FP INCONS	2105	<	2355
Total FP COMP	230	>	106
Total FN	4284	<	5421
P-value	3.56938820447e-08

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Performance plots

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

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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	3322
Total TN	15811989
Total FP	2705
Total FP CONTRA	370
Total FP INCONS	2105
Total FP COMP	230
Total FN	4284

Total Scores
MCC	0.500
Average MCC ± 95% Confidence Intervals	0.526 ± 0.056
Sensitivity	0.437
Positive Predictive Value	0.573
Nr of predictions	87

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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
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KFC_A	-	0.45	0.25	0.83	5	624	1	0	1	0	15
2KRL_A	-	0.76	0.60	0.96	24	5126	5	0	1	4	16
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.39	0.26	0.63	5	622	3	1	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.45	0.35	0.58	7	1528	5	2	3	0	13
2LKR_A	-	0.84	0.79	0.89	31	6070	6	0	4	2	8
2M58_A	-	-0.01	0.00	0.00	0	1640	13	0	13	0	17
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
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_D	-	0.39	0.23	0.67	6	1944	3	2	1	0	20
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
2WWQ_V	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	4	0	2	2	9
2XQD_Y	tRNA links to Rfam database...	0.78	0.70	0.86	19	2828	3	0	3	0	8
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
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
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
3GX2_A	SAM links to Rfam database...	0.77	0.63	0.96	25	4345	2	0	1	1	15
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_a	-	0.50	0.44	0.58	7	1116	5	2	3	0	9
3J0L_2	-	0.25	0.24	0.28	8	6187	26	0	21	5	25
3J0L_g	-	0.00	0.00	0.00	0	464	1	1	0	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J16_L	tRNA links to Rfam database...	0.46	0.40	0.55	12	2753	10	1	9	0	18
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	4	0	0	4	2
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.58	0.51	0.66	321	1116277	172	10	157	5	312
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J2C_M	-	0.43	0.34	0.53	71	106357	66	9	54	3	136
3J2C_O	-	0.79	0.67	0.93	42	10251	4	0	3	1	21
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.49	0.65	26	7835	16	0	14	2	27
3J3D_C	tRNA links to Rfam database...	0.67	0.61	0.74	17	2752	6	0	6	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.10	2	7483	32	1	17	14	31
3J3E_7	5S_rRNA links to Rfam database...	0.45	0.37	0.56	20	7104	16	1	15	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.33	0.29	12	12205	41	4	25	12	24
3J3F_7	5S_rRNA links to Rfam database...	0.68	0.62	0.76	31	7219	11	0	10	1	19
3J3V_B	5S_rRNA links to Rfam database...	0.48	0.39	0.61	22	6985	14	1	13	0	35
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_5	-	0.36	0.35	0.37	311	5022016	626	153	385	88	582
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
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
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
3PDR_A	ykoK links to Rfam database...	0.69	0.60	0.80	43	12826	13	0	11	2	29
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	2	7	0	22
3U4M_B	-	0.59	0.46	0.77	17	3138	5	0	5	0	20
3UZL_B	tRNA links to Rfam database...	0.70	0.54	0.91	20	3548	2	0	2	0	17
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.89	0.80	1.00	32	4721	1	0	0	1	8
3ZEX_G	-	0.28	0.24	0.33	18	16416	41	2	35	4	56
3ZEX_E	-	0.00	0.00	0.00	0	21889	58	4	52	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.67	0.80	33	6980	8	1	7	0	16
3ZEX_B	-	0.22	0.18	0.26	100	1071996	294	23	261	10	458
3ZEX_H	-	0.17	0.18	0.17	7	9003	35	6	29	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.28	0.21	0.38	11	14167	22	3	15	4	41
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZND_W	tRNA links to Rfam database...	0.19	0.22	0.18	5	2975	25	1	22	2	18
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.57	0.78	31	7100	9	1	8	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4AOB_A	SAM links to Rfam database...	0.44	0.36	0.56	15	4344	13	1	11	1	27
4ATO_G	-	0.44	0.40	0.50	4	520	4	0	4	0	6
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1314	1	1	0	0	8
4FNJ_A	-	0.79	0.63	1.00	10	585	0	0	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.68	0.56	0.82	18	3464	4	1	3	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.65	0.56	0.77	20	5125	6	1	5	0	16
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.34	0.30	0.39	7	1522	11	0	11	0	16

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Performance of McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	2185
Total TN	15813026
Total FP	2681
Total FP CONTRA	220
Total FP INCONS	2355
Total FP COMP	106
Total FN	5421

Total Scores
MCC	0.363
Average MCC ± 95% Confidence Intervals	0.484 ± 0.064
Sensitivity	0.287
Positive Predictive Value	0.459
Nr of predictions	87

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
2KFC_A	-	0.49	0.25	1.00	5	625	0	0	0	0	15
2KRL_A	-	0.59	0.53	0.68	21	5120	13	3	7	3	19
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
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
2LKR_A	-	0.51	0.46	0.58	18	6074	13	2	11	0	21
2M58_A	-	0.56	0.47	0.67	8	1641	4	1	3	0	9
2RP0_A	-	0.64	0.42	1.00	5	346	0	0	0	0	7
2WDL_A	-	0.31	0.26	0.37	308	3937383	531	27	503	1	896
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_D	-	0.32	0.23	0.46	6	1940	7	2	5	0	20
2WW9_F	-	0.71	0.60	0.86	6	293	1	0	1	0	4
2WW9_E	-	-0.01	0.00	0.00	0	556	5	0	5	0	14
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	28
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
2ZZM_B	tRNA links to Rfam database...	0.21	0.19	0.24	6	3461	19	2	17	0	26
2ZZN_D	tRNA links to Rfam database...	0.84	0.78	0.91	21	2462	2	0	2	0	6
3A2K_C	tRNA links to Rfam database...	0.86	0.75	1.00	21	2905	0	0	0	0	7
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	1	0	0	1	6
3AKZ_H	tRNA links to Rfam database...	0.68	0.61	0.77	17	2679	6	1	4	1	11
3AM1_B	-	0.91	0.83	1.00	29	3211	1	0	0	1	6
3AMU_B	tRNA links to Rfam database...	0.75	0.59	0.94	16	2986	3	0	1	2	11
3G4S_9	5S_rRNA links to Rfam database...	0.27	0.21	0.36	12	7348	21	1	20	0	45
3GCA_A	-	0.54	0.29	1.00	5	523	0	0	0	0	12
3GX2_A	SAM links to Rfam database...	0.47	0.40	0.57	16	4343	13	1	11	1	24
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...	0.20	0.18	0.24	6	4253	19	2	17	0	27
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60614	87	19	64	4	65
3IZ4_A	tmRNA links to Rfam database...	0.42	0.36	0.49	47	70780	53	6	43	4	85
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J0L_a	-	0.26	0.19	0.38	3	1120	5	1	4	0	13
3J0L_2	-	0.26	0.24	0.30	8	6189	21	0	19	2	25
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1215	10	0	10	0	17
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.46	0.39	0.54	249	1116304	216	8	204	4	384
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J2C_M	-	0.31	0.25	0.38	51	106357	86	12	71	3	156
3J2C_O	-	0.53	0.43	0.66	27	10255	15	1	13	1	36
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7479	36	3	21	12	33
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3F_8	5_8S_rRNA links to Rfam database...	0.30	0.31	0.30	11	12209	38	4	22	12	25
3J3F_7	5S_rRNA links to Rfam database...	0.18	0.16	0.22	8	7223	29	1	28	0	42
3J3V_B	5S_rRNA links to Rfam database...	0.49	0.33	0.73	19	6995	7	0	7	0	38
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2830	20	0	20	0	32
3JYX_5	-	0.00	0.00	0.00	0	5022865	0	0	0	0	893
3JYX_3	5S_rRNA links to Rfam database...	0.21	0.22	0.20	6	6298	24	9	15	0	21
3JYX_4	5_8S_rRNA links to Rfam database...	0.20	0.21	0.19	7	12210	33	8	21	4	26
3KIY_A	-	0.31	0.26	0.38	317	4053291	529	22	498	9	924
3KTW_C	-	0.36	0.30	0.45	13	4531	17	1	15	1	30
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.81	0.70	0.93	43	9134	4	1	2	1	18
3NKB_B	-	0.36	0.31	0.44	8	1998	10	1	9	0	18
3NPB_A	SAM links to Rfam database...	0.81	0.67	0.97	31	6989	4	1	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.26	0.26	0.26	9	12368	26	10	16	0	26
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3PDR_A	ykoK links to Rfam database...	0.69	0.56	0.87	40	12834	9	0	6	3	32
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...	0.71	0.60	0.86	25	3887	4	0	4	0	17
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
3W1K_J	tRNA-Sec links to Rfam database...	0.78	0.63	0.96	24	4161	1	1	0	0	14
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.54	15	4725	14	0	13	1	25
3ZEX_G	-	0.31	0.27	0.36	20	16416	38	1	34	3	54
3ZEX_E	-	0.00	0.00	0.00	0	21894	53	4	47	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.53	0.90	26	6992	3	1	2	0	23
3ZEX_B	-	0.11	0.09	0.13	53	1071960	373	32	335	6	505
3ZEX_H	-	0.21	0.21	0.22	8	9009	29	6	22	1	30
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.21	0.34	11	14164	24	2	19	3	41
3ZEX_F	-	0.00	0.00	0.00	0	2619	9	2	7	0	12
3ZND_W	tRNA links to Rfam database...	0.20	0.22	0.19	5	2977	23	1	20	2	18
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
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ATO_G	-	-0.01	0.00	0.00	0	523	5	0	5	0	10
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
4FNJ_A	-	-0.02	0.00	0.00	0	588	7	0	7	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11
4FRN_A	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	20	5130	1	1	0	0	16
4JF2_A	preQ1-II links to Rfam database...	0.83	0.81	0.86	25	2821	4	3	1	0	6
4JRC_A	-	0.83	0.70	1.00	16	1524	0	0	0	0	7

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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 McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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