CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(seed)		RNAshapes
MCC	0.686	>	0.669
Average MCC ± 95% Confidence Intervals	0.634 ± 0.061	<	0.691 ± 0.071
Sensitivity	0.535	<	0.693
Positive Predictive Value	0.884	>	0.653
Total TP	803	<	1040
Total TN	149442	>	148757
Total FP	204	<	802
Total FP CONTRA	43	<	164
Total FP INCONS	62	<	389
Total FP COMP	99	<	249
Total FN	698	>	461
P-value	6.58294707158e-07

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Performance plots

Comparison of performance of CentroidAlifold(seed) and RNAshapes. 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 CentroidAlifold(seed) and RNAshapes).
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 CentroidAlifold(seed) and RNAshapes).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and RNAshapes. 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 CentroidAlifold(seed) and RNAshapes).

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Performance of CentroidAlifold(seed) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	803
Total TN	149442
Total FP	204
Total FP CONTRA	43
Total FP INCONS	62
Total FP COMP	99
Total FN	698

Total Scores
MCC	0.686
Average MCC ± 95% Confidence Intervals	0.634 ± 0.061
Sensitivity	0.535
Positive Predictive Value	0.884
Nr of predictions	60

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2. Individual counts for CentroidAlifold(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...	0.44	0.44	0.47	8	450	10	0	9	1	10
2KUR_A	K10_TLS links to Rfam database...	0.77	0.74	0.82	14	450	4	0	3	1	5
2KUU_A	K10_TLS links to Rfam database...	0.88	0.83	0.94	15	431	3	0	1	2	3
2KUV_A	K10_TLS links to Rfam database...	0.46	0.47	0.50	9	421	9	0	9	0	10
2KUW_A	K10_TLS links to Rfam database...	0.44	0.44	0.47	8	453	10	0	9	1	10
2KX8_A	7SK links to Rfam database...	0.00	0.00	0.00	0	371	0	0	0	0	16
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...	0.51	0.50	0.56	9	341	8	0	7	1	9
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	528	0	0	0	0	18
2WRQ_Y	tRNA links to Rfam database...	0.47	0.22	1.00	2	1150	4	0	0	4	7
2WWQ_V	tRNA links to Rfam database...	0.56	0.32	1.00	6	1198	0	0	0	0	13
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.67	0.73	0.62	8	1822	22	0	5	17	3
2XQD_Y	tRNA links to Rfam database...	0.48	0.24	1.00	5	1124	1	0	0	1	16
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.83	0.74	0.93	26	2017	4	0	2	2	9
2ZZM_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1358	6	0	0	6	15
2ZZN_D	tRNA links to Rfam database...	0.52	0.27	1.00	6	978	0	0	0	0	16
3A2K_C	tRNA links to Rfam database...	0.52	0.27	1.00	6	1102	0	0	0	0	16
3A3A_A	tRNA-Sec links to Rfam database...	0.95	0.90	1.00	27	1473	0	0	0	0	3
3AKZ_H	tRNA links to Rfam database...	0.50	0.25	1.00	5	1122	1	0	0	1	15
3AMU_B	tRNA links to Rfam database...	0.51	0.26	1.00	5	1152	1	0	0	1	14
3GX2_A	SAM links to Rfam database...	0.92	0.86	1.00	24	1425	1	0	0	1	4
3IVN_B	Purine links to Rfam database...	0.86	0.83	0.90	19	882	2	2	0	0	4
3IYQ_A	tmRNA links to Rfam database...	0.56	0.55	0.57	28	22391	30	19	2	9	23
3IZ4_A	tmRNA links to Rfam database...	0.58	0.43	0.77	41	25483	17	12	0	5	54
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.46	1.00	16	2624	0	0	0	0	19
3J16_L	tRNA links to Rfam database...	0.53	0.29	1.00	6	1153	0	0	0	0	15
3J20_0	tRNA links to Rfam database...	0.53	0.29	1.00	6	1213	0	0	0	0	15
3J20_1	tRNA links to Rfam database...	0.54	0.30	1.00	6	1106	0	0	0	0	14
3J2L_3	5S_rRNA links to Rfam database...	0.66	0.44	1.00	15	3005	2	0	0	2	19
3J3D_C	tRNA links to Rfam database...	0.56	0.32	1.00	6	962	0	0	0	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.39	0.20	0.75	3	2738	1	1	0	0	12
3J3E_7	5S_rRNA links to Rfam database...	0.68	0.50	0.94	17	2723	2	0	1	1	17
3J3F_8	5_8S_rRNA links to Rfam database...	0.62	0.47	0.82	9	4750	4	2	0	2	10
3J3F_7	5S_rRNA links to Rfam database...	0.68	0.47	1.00	17	2917	1	0	0	1	19
3J3V_B	5S_rRNA links to Rfam database...	0.61	0.44	0.86	12	2642	7	0	2	5	15
3JYV_7	tRNA links to Rfam database...	0.50	0.25	1.00	5	1106	1	0	0	1	15
3JYX_4	5_8S_rRNA links to Rfam database...	0.91	0.83	1.00	10	4746	3	0	0	3	2
3JYX_3	5S_rRNA links to Rfam database...	0.65	0.53	0.80	8	2368	8	0	2	6	7
3LA5_A	Purine links to Rfam database...	0.87	0.80	0.95	20	933	1	1	0	0	5
3NPB_A	SAM links to Rfam database...	0.79	0.65	0.96	24	2253	5	0	1	4	13
3O58_2	5S_rRNA links to Rfam database...	0.72	0.52	1.00	16	2738	0	0	0	0	15
3O58_3	5_8S_rRNA links to Rfam database...	0.68	0.50	0.92	11	4752	2	1	0	1	11
3PDR_A	ykoK links to Rfam database...	0.93	0.88	0.98	44	4795	3	0	1	2	6
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...	0.85	0.76	0.96	22	1510	1	0	1	0	7
3UZL_B	tRNA links to Rfam database...	0.50	0.25	1.00	4	1289	2	0	0	2	12
3W1K_J	tRNA-Sec links to Rfam database...	0.86	0.81	0.93	25	1651	2	1	1	0	6
3W3S_B	tRNA-Sec links to Rfam database...	0.80	0.70	0.92	23	1964	4	0	2	2	10
3ZEX_D	5S_rRNA links to Rfam database...	0.65	0.43	1.00	15	2781	3	0	0	3	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.56	0.34	0.91	10	5363	3	1	0	2	19
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	1189	6	0	2	4	8
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.43	1.00	16	2747	0	0	0	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENB_A	crcB links to Rfam database...	0.72	0.53	1.00	8	464	0	0	0	0	7
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.71	0.94	17	1184	2	0	1	1	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...	0.76	0.63	0.94	15	1066	1	1	0	0	9

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Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	1040
Total TN	148757
Total FP	802
Total FP CONTRA	164
Total FP INCONS	389
Total FP COMP	249
Total FN	461

Total Scores
MCC	0.669
Average MCC ± 95% Confidence Intervals	0.691 ± 0.071
Sensitivity	0.693
Positive Predictive Value	0.653
Nr of predictions	60

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2. Individual counts for RNAshapes [ 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...	0.97	0.94	1.00	15	356	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.89	0.87	0.91	20	741	2	0	2	0	3
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	768	0	0	0	0	1
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	0	5	0	7
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	5	0	0	5	0
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.64	0.73	0.57	8	1821	24	0	6	18	3
2XQD_Y	tRNA links to Rfam database...	0.70	0.67	0.74	14	1110	6	0	5	1	7
2XXA_G	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	35	2010	1	0	0	1	0
2ZZM_B	tRNA links to Rfam database...	0.05	0.07	0.06	1	1340	25	4	13	8	14
2ZZN_D	tRNA links to Rfam database...	0.77	0.77	0.77	17	962	5	1	4	0	5
3A2K_C	tRNA links to Rfam database...	0.47	0.50	0.46	11	1084	13	3	10	0	11
3A3A_A	tRNA-Sec links to Rfam database...	0.84	0.80	0.89	24	1473	3	0	3	0	6
3AKZ_H	tRNA links to Rfam database...	0.78	0.80	0.76	16	1106	7	2	3	2	4
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...	0.91	0.89	0.93	25	1422	3	1	1	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...	0.19	0.27	0.14	14	22340	95	43	43	9	37
3IZ4_A	tmRNA links to Rfam database...	0.57	0.58	0.56	55	25437	50	16	28	6	40
3IZF_C	5S_rRNA links to Rfam database...	0.76	0.77	0.75	27	2604	14	0	9	5	8
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...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.77	0.79	0.75	27	2984	14	1	8	5	7
3J3D_C	tRNA links to Rfam database...	0.63	0.68	0.59	13	946	9	3	6	0	6
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	29	6	13	10	10
3J3E_7	5S_rRNA links to Rfam database...	0.64	0.65	0.65	22	2707	16	1	11	4	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.26	8	4730	42	11	12	19	11
3J3F_7	5S_rRNA links to Rfam database...	0.83	0.81	0.85	29	2900	7	0	5	2	7
3J3V_B	5S_rRNA links to Rfam database...	0.23	0.26	0.23	7	2625	27	4	20	3	20
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1092	20	1	18	1	20
3JYX_4	5_8S_rRNA links to Rfam database...	0.61	0.83	0.45	10	4734	35	10	2	23	2
3JYX_3	5S_rRNA links to Rfam database...	0.77	0.80	0.75	12	2362	26	0	4	22	3
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.84	0.76	0.93	28	2248	5	1	1	3	9
3O58_2	5S_rRNA links to Rfam database...	0.73	0.74	0.72	23	2722	18	0	9	9	8
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	38	6	15	17	11
3PDR_A	ykoK links to Rfam database...	0.80	0.80	0.80	40	4790	12	3	7	2	10
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3UZL_B	tRNA links to Rfam database...	0.43	0.50	0.38	8	1272	17	4	9	4	8
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...	0.60	0.58	0.63	19	1959	12	2	9	1	14
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.80	0.93	28	2766	6	0	2	4	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.29	0.34	0.26	10	5335	42	5	24	13	19
3ZND_W	tRNA links to Rfam database...	0.24	0.38	0.16	3	1172	24	9	7	8	5
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	7	0	4	3	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	11	16	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
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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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 CentroidAlifold(seed) - scored higher in this pairwise comparison

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

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

Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

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