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		CentroidFold
MCC	0.488	>	0.483
Average MCC ± 95% Confidence Intervals	0.523 ± 0.059	>	0.511 ± 0.058
Sensitivity	0.430	>	0.397
Positive Predictive Value	0.556	<	0.587
Total TP	2701	>	2496
Total TN	11865408	<	11866016
Total FP	2386	>	1922
Total FP CONTRA	336	>	288
Total FP INCONS	1824	>	1469
Total FP COMP	226	>	165
Total FN	3584	<	3789
P-value	5.21776328505e-08

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Performance plots

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

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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	2701
Total TN	11865408
Total FP	2386
Total FP CONTRA	336
Total FP INCONS	1824
Total FP COMP	226
Total FN	3584

Total Scores
MCC	0.488
Average MCC ± 95% Confidence Intervals	0.523 ± 0.059
Sensitivity	0.430
Positive Predictive Value	0.556
Nr of predictions	81

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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
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
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
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
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
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_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
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_a	-	0.50	0.44	0.58	7	1116	5	2	3	0	9
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_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.58	0.51	0.66	321	1116277	172	10	157	5	312
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_7	5S_rRNA links to Rfam database...	0.45	0.37	0.56	20	7104	16	1	15	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.06	0.10	2	7483	32	1	17	14	31
3J3F_7	5S_rRNA links to Rfam database...	0.68	0.62	0.76	31	7219	11	0	10	1	19
3J3F_8	5_8S_rRNA links to Rfam database...	0.31	0.33	0.29	12	12205	41	4	25	12	24
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_3	5S_rRNA links to Rfam database...	0.28	0.30	0.27	8	6298	23	8	14	1	19
3JYX_5	-	0.36	0.35	0.37	311	5022016	626	153	385	88	582
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_2	5S_rRNA links to Rfam database...	0.78	0.76	0.81	29	7224	10	2	5	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.26	0.31	9	12374	20	3	17	0	26
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_E	-	0.00	0.00	0.00	0	21889	58	4	52	2	77
3ZEX_G	-	0.28	0.24	0.33	18	16416	41	2	35	4	56
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_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11751	33	5	20	8	28
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.57	0.78	31	7100	9	1	8	0	23
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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	2496
Total TN	11866016
Total FP	1922
Total FP CONTRA	288
Total FP INCONS	1469
Total FP COMP	165
Total FN	3789

Total Scores
MCC	0.483
Average MCC ± 95% Confidence Intervals	0.511 ± 0.058
Sensitivity	0.397
Positive Predictive Value	0.587
Nr of predictions	81

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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	-	0.42	0.26	0.71	5	623	2	0	2	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.49	0.35	0.70	7	1530	3	1	2	0	13
2LKR_A	-	0.82	0.74	0.91	29	6073	4	0	3	1	10
2M58_A	-	0.09	0.06	0.14	1	1646	6	0	6	0	16
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	12	5	3	4	7
2WW9_E	-	0.00	0.00	0.00	0	561	0	0	0	0	14
2WW9_F	-	0.59	0.60	0.60	6	290	4	0	4	0	4
2WW9_D	-	0.29	0.12	0.75	3	1949	1	0	1	0	23
2WWQ_V	tRNA links to Rfam database...	0.80	0.68	0.95	19	2906	3	0	1	2	9
2XQD_Y	tRNA links to Rfam database...	0.75	0.67	0.86	18	2829	3	0	3	0	9
2ZZM_B	tRNA links to Rfam database...	0.18	0.16	0.23	5	3464	17	3	14	0	27
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...	0.43	0.39	0.48	11	2678	12	2	10	0	17
3AM1_B	-	0.68	0.63	0.73	22	3210	8	1	7	0	13
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3GX2_A	SAM links to Rfam database...	0.79	0.63	1.00	25	4346	1	0	0	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...	0.36	0.37	0.34	35	60624	71	17	50	4	59
3IZ4_A	tmRNA links to Rfam database...	0.55	0.45	0.68	59	70789	33	4	24	5	73
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.61	0.77	33	6860	10	1	9	0	21
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_2	-	0.25	0.24	0.28	8	6187	24	0	21	3	25
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_a	-	0.41	0.31	0.56	5	1119	4	2	2	0	11
3J16_L	tRNA links to Rfam database...	0.50	0.40	0.63	12	2756	7	0	7	0	18
3J20_1	tRNA links to Rfam database...	0.91	0.87	0.95	20	2905	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.44	0.40	0.50	12	2826	13	0	12	1	18
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.56	0.48	0.67	303	1116310	158	8	144	6	330
3J2C_M	-	0.40	0.29	0.57	59	106387	47	5	40	2	148
3J2C_O	-	0.76	0.65	0.89	41	10250	6	0	5	1	22
3J2L_3	5S_rRNA links to Rfam database...	0.53	0.49	0.58	26	7830	21	0	19	2	27
3J3D_C	tRNA links to Rfam database...	0.49	0.43	0.57	12	2754	9	0	9	0	16
3J3E_7	5S_rRNA links to Rfam database...	0.46	0.37	0.59	20	7106	14	1	13	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7485	21	2	16	3	33
3J3F_7	5S_rRNA links to Rfam database...	0.20	0.18	0.23	9	7221	30	1	29	0	41
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.34	12	12211	34	4	19	11	24
3J3V_B	5S_rRNA links to Rfam database...	0.47	0.37	0.60	21	6986	14	1	13	0	36
3JYV_7	tRNA links to Rfam database...	0.77	0.59	1.00	19	2831	0	0	0	0	13
3JYX_3	5S_rRNA links to Rfam database...	0.29	0.30	0.30	8	6301	20	8	11	1	19
3JYX_5	-	0.36	0.33	0.40	294	5022122	510	149	300	61	599
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.21	0.25	7	12218	25	5	16	4	26
3KIY_A	-	0.53	0.41	0.69	505	4053393	246	24	206	16	736
3KTW_C	-	0.45	0.40	0.53	17	4528	16	2	13	1	26
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NDB_M	-	0.80	0.70	0.91	43	9133	5	0	4	1	18
3NKB_B	-	0.57	0.50	0.65	13	1996	7	0	7	0	13
3NPB_A	SAM links to Rfam database...	0.77	0.70	0.86	32	6984	7	1	4	2	14
3O58_2	5S_rRNA links to Rfam database...	0.82	0.76	0.88	29	7227	7	1	3	3	9
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.29	0.50	10	12383	10	0	10	0	25
3PDR_A	ykoK links to Rfam database...	0.73	0.60	0.90	43	12832	7	0	5	2	29
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
3U4M_B	-	0.57	0.46	0.71	17	3136	7	0	7	0	20
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
3W1K_J	tRNA-Sec links to Rfam database...	0.56	0.50	0.63	19	4156	11	2	9	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.78	0.97	31	4721	2	0	1	1	9
3ZEX_E	-	0.00	0.00	0.00	0	21895	52	3	47	2	77
3ZEX_G	-	0.36	0.28	0.46	21	16425	29	2	23	4	53
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.59	0.91	29	6989	3	0	3	0	20
3ZEX_B	-	0.23	0.16	0.34	87	1072121	178	9	163	6	471
3ZEX_H	-	0.19	0.18	0.21	7	9011	27	4	23	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.47	0.27	0.82	14	14179	3	1	2	0	38
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_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.56	0.81	30	7103	7	1	6	0	24
4AOB_A	SAM links to Rfam database...	0.45	0.33	0.61	14	4348	10	1	8	1	28
4ATO_G	-	0.31	0.20	0.50	2	524	2	0	2	0	8
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	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	-	0.15	0.13	0.22	2	586	7	0	7	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.24	0.22	0.28	7	3461	18	3	15	0	25
4FRN_A	AdoCbl-variant links to Rfam database...	0.40	0.28	0.59	10	5134	7	2	5	0	26
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12
4JRC_A	-	0.81	0.70	0.94	16	1523	1	0	1	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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

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