CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidFold		RSpredict(seed)
MCC	0.718	>	0.446
Average MCC ± 95% Confidence Intervals	0.736 ± 0.068	>	0.244 ± 0.084
Sensitivity	0.718	>	0.302
Positive Predictive Value	0.720	>	0.664
Total TP	1354	>	569
Total TN	568182	<	569205
Total FP	764	>	380
Total FP CONTRA	178	>	55
Total FP INCONS	348	>	233
Total FP COMP	238	>	92
Total FN	532	<	1317
P-value	3.56938820447e-08

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Performance plots

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

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Performance of CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	1354
Total TN	568182
Total FP	764
Total FP CONTRA	178
Total FP INCONS	348
Total FP COMP	238
Total FN	532

Total Scores
MCC	0.718
Average MCC ± 95% Confidence Intervals	0.736 ± 0.068
Sensitivity	0.718
Positive Predictive Value	0.720
Nr of predictions	60

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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
2KE6_A	K10_TLS links to Rfam database...	1.00	1.00	1.00	18	449	1	0	0	1	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
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	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
2LC8_A	GP_knot1 links to Rfam database...	0.51	0.39	0.70	7	518	3	1	2	0	11
2WRQ_Y	tRNA links to Rfam database...	1.00	1.00	1.00	9	1143	13	0	0	13	0
2WWQ_V	tRNA links to Rfam database...	1.00	1.00	1.00	19	1185	3	0	0	3	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	27	0	6	21	3
2XQD_Y	tRNA links to Rfam database...	0.83	0.81	0.85	17	1109	4	0	3	1	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.13	0.11	0.17	4	2021	21	2	18	1	31
2ZZM_B	tRNA links to Rfam database...	0.13	0.13	0.15	2	1345	20	3	8	9	13
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
3AKZ_H	tRNA links to Rfam database...	0.48	0.50	0.48	10	1106	13	3	8	2	10
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	4
3GX2_A	SAM links to Rfam database...	0.94	0.89	1.00	25	1424	1	0	0	1	3
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.29	0.39	0.22	20	22347	86	39	34	13	31
3IZ4_A	tmRNA links to Rfam database...	0.60	0.57	0.64	54	25451	38	16	15	7	41
3IZF_C	5S_rRNA links to Rfam database...	0.89	0.91	0.86	32	2603	11	0	5	6	3
3J16_L	tRNA links to Rfam database...	0.59	0.57	0.63	12	1140	7	0	7	0	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	2	0	0	2	0
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.70	0.69	0.70	286	421962	177	23	97	57	126
3J2L_3	5S_rRNA links to Rfam database...	0.74	0.76	0.72	26	2984	15	1	9	5	8
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.59	0.65	20	2710	13	2	9	2	14
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.13	0.13	2	2726	22	4	10	8	13
3J3F_7	5S_rRNA links to Rfam database...	0.84	0.86	0.82	31	2896	9	1	6	2	5
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	37	12	11	14	10
3JYV_7	tRNA links to Rfam database...	0.92	0.85	1.00	17	1094	2	0	0	2	3
3JYX_4	5_8S_rRNA links to Rfam database...	0.41	0.58	0.29	7	4732	25	11	6	8	5
3JYX_3	5S_rRNA links to Rfam database...	0.35	0.47	0.27	7	2352	21	14	5	2	8
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NPB_A	SAM links to Rfam database...	0.87	0.84	0.91	31	2244	8	1	2	5	6
3O58_2	5S_rRNA links to Rfam database...	0.95	0.94	0.97	29	2724	7	0	1	6	2
3O58_3	5_8S_rRNA links to Rfam database...	0.44	0.41	0.47	9	4745	11	1	9	1	13
3PDR_A	ykoK links to Rfam database...	0.88	0.86	0.90	43	4792	7	2	3	2	7
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.70	0.69	0.71	20	1505	8	4	4	0	9
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.95	0.91	1.00	30	1959	1	0	0	1	3
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.34	0.67	10	5359	6	1	4	1	19
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.86	0.91	30	2763	8	0	3	5	5
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	25	9	7	9	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	29	9	12	8	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	8	0	6	2	8
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	1	0	0	1	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	1	0	0	1	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.80	0.71	0.91	20	1826	2	1	1	0	8
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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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	569
Total TN	569205
Total FP	380
Total FP CONTRA	55
Total FP INCONS	233
Total FP COMP	92
Total FN	1317

Total Scores
MCC	0.446
Average MCC ± 95% Confidence Intervals	0.244 ± 0.084
Sensitivity	0.302
Positive Predictive Value	0.664
Nr of predictions	60

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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
2KE6_A	K10_TLS links to Rfam database...	0.85	0.78	0.93	14	452	2	0	1	1	4
2KUR_A	K10_TLS links to Rfam database...	0.86	0.79	0.94	15	451	1	0	1	0	4
2KUU_A	K10_TLS links to Rfam database...	0.85	0.78	0.93	14	432	2	0	1	1	4
2KUV_A	K10_TLS links to Rfam database...	0.85	0.79	0.94	15	423	1	0	1	0	4
2KUW_A	K10_TLS links to Rfam database...	0.75	0.67	0.86	12	456	3	0	2	1	6
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	370	1	0	1	0	16
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.78	0.86	18	742	3	0	3	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.87	0.83	0.91	20	769	2	0	2	0	4
2L94_A	HIV_FE links to Rfam database...	0.55	0.50	0.64	9	343	6	0	5	1	9
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
2WRQ_Y	tRNA links to Rfam database...	0.00	0.00	0.00	0	1150	3	1	1	1	9
2WWQ_V	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1199	6	0	5	1	19
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.36	0.40	4	1825	8	4	2	2	7
2XQD_Y	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1124	5	0	5	0	21
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.37	0.20	0.70	7	2035	3	0	3	0	28
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1358	4	0	0	4	15
2ZZN_D	tRNA links to Rfam database...	0.38	0.18	0.80	4	979	1	1	0	0	18
3A2K_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1106	2	0	2	0	22
3A3A_A	tRNA-Sec links to Rfam database...	0.53	0.37	0.79	11	1486	3	0	3	0	19
3AKZ_H	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1125	2	0	2	0	20
3AMU_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1155	2	0	2	0	19
3GX2_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1442	1	0	1	0	22
3IVN_B	Purine links to Rfam database...	0.81	0.70	0.94	16	886	1	1	0	0	7
3IYQ_A	tmRNA links to Rfam database...	0.16	0.10	0.26	5	22421	21	10	4	7	46
3IZ4_A	tmRNA links to Rfam database...	0.26	0.11	0.63	10	25520	7	2	4	1	85
3IZF_C	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2635	5	0	5	0	35
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3J20_0	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1215	4	0	4	0	21
3J20_1	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1108	5	0	4	1	20
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.77	0.76	0.78	312	421966	152	18	72	62	100
3J2L_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	3015	5	0	5	0	34
3J3D_C	tRNA links to Rfam database...	-0.01	0.00	0.00	0	964	4	1	3	0	19
3J3E_7	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2733	8	1	7	0	34
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3F_7	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2930	4	1	3	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	5	3	1	1	17
3JYV_7	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1108	4	0	3	1	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4754	5	0	2	3	12
3JYX_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2373	5	1	4	0	15
3LA5_A	Purine links to Rfam database...	0.82	0.68	1.00	17	937	0	0	0	0	8
3NPB_A	SAM links to Rfam database...	-0.01	0.00	0.00	0	2274	4	0	4	0	37
3O58_2	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2751	3	0	3	0	31
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.14	0.60	3	4759	2	0	2	0	19
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	4832	8	0	8	0	50
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3UZL_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1287	6	3	3	0	16
3W1K_J	tRNA-Sec links to Rfam database...	0.57	0.35	0.92	11	1666	1	0	1	0	20
3W3S_B	tRNA-Sec links to Rfam database...	0.45	0.36	0.57	12	1968	10	1	8	1	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.13	0.07	0.25	2	5366	6	2	4	0	27
3ZEX_D	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2794	2	0	2	0	35
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	1189	4	0	2	2	8
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	-0.01	0.00	0.00	0	1200	2	0	2	0	24
4FRN_A	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1845	3	0	3	0	28
4JF2_A	preQ1-II links to Rfam database...	-0.01	0.00	0.00	0	1078	4	0	4	0	24

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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 CentroidFold - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidFold

2. Individual counts for CentroidFold [ 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 ]