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		RSpredict(seed)
MCC	0.589	>	0.375
Average MCC ± 95% Confidence Intervals	0.627 ± 0.066	>	0.235 ± 0.079
Sensitivity	0.528	>	0.220
Positive Predictive Value	0.660	>	0.642
Total TP	1453	>	606
Total TN	1507099	<	1508357
Total FP	857	>	351
Total FP CONTRA	99	>	25
Total FP INCONS	650	>	313
Total FP COMP	108	>	13
Total FN	1301	<	2148
P-value	3.56938820447e-08

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Performance plots

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

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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	1453
Total TN	1507099
Total FP	857
Total FP CONTRA	99
Total FP INCONS	650
Total FP COMP	108
Total FN	1301

Total Scores
MCC	0.589
Average MCC ± 95% Confidence Intervals	0.627 ± 0.066
Sensitivity	0.528
Positive Predictive Value	0.660
Nr of predictions	61

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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
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
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
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.45	0.35	0.58	7	1528	5	2	3	0	13
2WRQ_Y	tRNA links to Rfam database...	0.57	0.59	0.56	10	2832	13	5	3	5	7
2WWQ_V	tRNA links to Rfam database...	0.78	0.68	0.90	19	2905	4	0	2	2	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.51	0.50	0.53	10	4541	25	0	9	16	10
2XQD_Y	tRNA links to Rfam database...	0.78	0.70	0.86	19	2828	3	0	3	0	8
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.13	0.12	0.15	5	5117	29	1	28	0	37
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
3AKZ_H	tRNA links to Rfam database...	0.39	0.39	0.41	11	2674	17	4	12	1	17
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
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
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
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_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
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
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	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
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_C	5_8S_rRNA links to Rfam database...	0.28	0.21	0.38	11	14167	22	3	15	4	41
3ZEX_D	5S_rRNA links to Rfam database...	0.73	0.67	0.80	33	6980	8	1	7	0	16
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
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
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

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Performance of RSpredict(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for RSpredict(seed)

Total Base Pair Counts
Total TP	606
Total TN	1508357
Total FP	351
Total FP CONTRA	25
Total FP INCONS	313
Total FP COMP	13
Total FN	2148

Total Scores
MCC	0.375
Average MCC ± 95% Confidence Intervals	0.235 ± 0.079
Sensitivity	0.220
Positive Predictive Value	0.642
Nr of predictions	61

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2. Individual counts for RSpredict(seed) [ 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...	0.85	0.73	1.00	8	398	0	0	0	0	3
2KE6_A	K10_TLS links to Rfam database...	0.83	0.74	0.93	14	1113	2	0	1	1	5
2KUR_A	K10_TLS links to Rfam database...	0.82	0.71	0.94	15	1112	1	0	1	0	6
2KUU_A	K10_TLS links to Rfam database...	0.79	0.67	0.93	14	1113	2	0	1	1	7
2KUV_A	K10_TLS links to Rfam database...	0.80	0.68	0.94	15	1112	1	0	1	0	7
2KUW_A	K10_TLS links to Rfam database...	0.73	0.62	0.87	13	1113	2	0	2	0	8
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	860	1	0	1	0	18
2L1F_A	Gammaretro_CES links to Rfam database...	0.80	0.75	0.86	18	2059	3	0	3	0	6
2L1F_B	Gammaretro_CES links to Rfam database...	0.85	0.80	0.91	20	2123	2	0	2	0	5
2L94_A	HIV_FE links to Rfam database...	0.57	0.50	0.67	10	975	5	0	5	0	10
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2848	3	1	1	1	17
2WWQ_V	tRNA links to Rfam database...	0.00	0.00	0.00	0	2920	6	1	5	0	28
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.28	0.20	0.40	4	4550	8	2	4	2	16
2XQD_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	2845	5	0	5	0	27
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.17	0.70	7	5141	3	0	3	0	35
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3482	4	0	4	0	32
2ZZN_D	tRNA links to Rfam database...	0.43	0.19	1.00	5	2480	0	0	0	0	22
3A2K_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2924	2	0	2	0	28
3A3A_A	tRNA-Sec links to Rfam database...	0.48	0.30	0.79	11	3641	3	0	3	0	26
3AKZ_H	tRNA links to Rfam database...	0.00	0.00	0.00	0	2699	2	0	2	0	28
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3001	2	0	2	0	27
3GX2_A	SAM links to Rfam database...	0.36	0.15	0.86	6	4364	1	0	1	0	34
3IVN_B	Purine links to Rfam database...	0.69	0.52	0.94	16	2329	1	0	1	0	15
3IYQ_A	tmRNA links to Rfam database...	0.14	0.07	0.28	7	60701	19	5	13	1	87
3IZ4_A	tmRNA links to Rfam database...	0.21	0.08	0.59	10	70859	7	0	7	0	122
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6898	5	0	5	0	54
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2774	1	0	1	0	30
3J20_1	tRNA links to Rfam database...	0.09	0.04	0.20	1	2921	4	0	4	0	22
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	30
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.62	0.53	0.73	335	1116304	129	9	117	3	298
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7870	5	0	5	0	53
3J3D_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	2771	4	1	3	0	28
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3E_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7132	8	0	8	0	54
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7256	4	0	4	0	50
3J3F_8	5_8S_rRNA links to Rfam database...	0.14	0.06	0.33	2	12240	5	1	3	1	34
3JYV_7	tRNA links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	32
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	6323	5	1	4	0	27
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12241	5	0	5	0	33
3LA5_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2468	0	0	0	0	17
3NPB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	7017	4	0	4	0	46
3O58_3	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12398	2	0	2	0	32
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7257	3	0	3	0	38
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12872	8	0	8	0	72
3RKF_A	Purine links to Rfam database...	0.71	0.53	0.95	18	2192	1	0	1	0	16
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3564	6	0	6	0	37
3W1K_J	tRNA-Sec links to Rfam database...	0.51	0.29	0.92	11	4174	1	0	1	0	27
3W3S_B	tRNA-Sec links to Rfam database...	0.41	0.30	0.57	12	4732	10	1	8	1	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.10	0.04	0.25	2	14188	6	1	5	0	50
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7019	2	0	2	0	49
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	3000	4	0	3	1	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11777	5	1	3	1	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7136	4	1	3	0	54
4AOB_A	SAM links to Rfam database...	0.35	0.14	0.86	6	4364	1	0	1	0	36
4ENB_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1270	2	0	2	0	16
4ENC_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1321	2	0	2	0	16
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	3484	2	0	2	0	32
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	5148	3	0	3	0	36
4JF2_A	preQ1-II links to Rfam database...	0.00	0.00	0.00	0	2846	4	0	4	0	31

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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 RSpredict(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for RSpredict(seed)

2. Individual counts for RSpredict(seed) [ download as .csv ]