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)		CentroidFold
MCC	0.733	>	0.718
Average MCC ± 95% Confidence Intervals	0.638 ± 0.060	<	0.736 ± 0.067
Sensitivity	0.602	<	0.718
Positive Predictive Value	0.894	>	0.720
Total TP	1152	<	1374
Total TN	571430	>	570810
Total FP	306	<	780
Total FP CONTRA	52	<	179
Total FP INCONS	84	<	355
Total FP COMP	170	<	246
Total FN	761	>	539
P-value	6.70530687003e-06

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Performance plots

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

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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	1152
Total TN	571430
Total FP	306
Total FP CONTRA	52
Total FP INCONS	84
Total FP COMP	170
Total FN	761

Total Scores
MCC	0.733
Average MCC ± 95% Confidence Intervals	0.638 ± 0.060
Sensitivity	0.602
Positive Predictive Value	0.894
Nr of predictions	61

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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_2	SSU_rRNA_archaea links to Rfam database...	0.88	0.85	0.92	349	421988	102	9	22	71	63
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_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.43	1.00	16	2747	0	0	0	0	21
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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	1374
Total TN	570810
Total FP	780
Total FP CONTRA	179
Total FP INCONS	355
Total FP COMP	246
Total FN	539

Total Scores
MCC	0.718
Average MCC ± 95% Confidence Intervals	0.736 ± 0.067
Sensitivity	0.718
Positive Predictive Value	0.720
Nr of predictions	61

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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_2	SSU_rRNA_archaea links to Rfam database...	0.70	0.69	0.70	286	421962	177	23	97	57	126
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
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_8	5_8S_rRNA links to Rfam database...	0.12	0.13	0.13	2	2726	22	4	10	8	13
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.59	0.65	20	2710	13	2	9	2	14
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	37	12	11	14	10
3J3F_7	5S_rRNA links to Rfam database...	0.84	0.86	0.82	31	2896	9	1	6	2	5
3J3V_B	5S_rRNA links to Rfam database...	0.72	0.74	0.71	20	2628	16	1	7	8	7
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_D	5S_rRNA links to Rfam database...	0.88	0.86	0.91	30	2763	8	0	3	5	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.48	0.34	0.67	10	5359	6	1	4	1	19
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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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 CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

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