CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		NanoFolder
MCC	0.537	>	0.176
Average MCC ± 95% Confidence Intervals	0.529 ± 0.038	>	0.175 ± 0.026
Sensitivity	0.335	>	0.203
Positive Predictive Value	0.861	>	0.156
Total TP	2662	>	1614
Total TN	4409509	>	4402260
Total FP	492	<	8930
Total FP CONTRA	64	<	1294
Total FP INCONS	364	<	7431
Total FP COMP	64	<	205
Total FN	5277	<	6325
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAalifold(seed) and NanoFolder. 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 RNAalifold(seed) and NanoFolder).
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 RNAalifold(seed) and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and NanoFolder. 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 RNAalifold(seed) and NanoFolder).

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

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

Total Base Pair Counts
Total TP	2662
Total TN	4409509
Total FP	492
Total FP CONTRA	64
Total FP INCONS	364
Total FP COMP	64
Total FN	5277

Total Scores
MCC	0.537
Average MCC ± 95% Confidence Intervals	0.529 ± 0.038
Sensitivity	0.335
Positive Predictive Value	0.861
Nr of predictions	78

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00017	RNaseP_nuc links to Rfam database...	0.51	0.31	0.83	20	51016	5	0	4	1	44
ASE_00083	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.79	23	62452	6	1	5	0	87
ASE_00122	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	43336	6	1	5	0	65
ASE_00185	RNaseP_bact_a links to Rfam database...	0.38	0.18	0.79	23	73507	6	1	5	0	105
ASE_00190	RNaseP_bact_b links to Rfam database...	0.66	0.50	0.87	45	45399	12	1	6	5	45
ASE_00191	RNaseP_arch links to Rfam database...	0.85	0.74	0.98	45	29600	1	0	1	0	16
ASE_00196	RNaseP_arch links to Rfam database...	0.77	0.63	0.96	47	31577	2	0	2	0	28
ASE_00221	RNaseP_bact_a links to Rfam database...	0.50	0.31	0.82	36	64576	8	1	7	0	81
ASE_00227	RNaseP_bact_a links to Rfam database...	0.37	0.20	0.68	27	78963	13	1	12	0	106
ASE_00228	RNaseP_bact_a links to Rfam database...	0.47	0.26	0.88	22	46946	3	0	3	0	64
ASE_00229	RNaseP_bact_a links to Rfam database...	0.47	0.25	0.88	22	42461	3	0	3	0	65
ASE_00231	RNaseP_bact_a links to Rfam database...	0.45	0.23	0.88	22	47870	3	0	3	0	74
ASE_00234	RNaseP_bact_a links to Rfam database...	0.35	0.17	0.73	22	75436	8	3	5	0	107
ASE_00238	RNaseP_bact_a links to Rfam database...	0.38	0.19	0.73	22	64231	8	3	5	0	92
ASE_00248	RNaseP_bact_a links to Rfam database...	0.51	0.32	0.82	36	62437	8	1	7	0	78
ASE_00250	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.81	35	78960	8	1	7	0	96
ASE_00254	RNaseP_bact_a links to Rfam database...	0.49	0.27	0.88	22	36831	3	0	3	0	60
ASE_00255	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.81	35	74648	8	1	7	0	95
ASE_00257	RNaseP_bact_a links to Rfam database...	0.43	0.24	0.79	23	51011	6	1	5	0	74
ASE_00267	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.79	23	45121	6	1	5	0	65
ASE_00270	RNaseP_bact_a links to Rfam database...	0.22	0.09	0.52	12	72367	12	1	10	1	116
ASE_00274	RNaseP_bact_a links to Rfam database...	0.40	0.21	0.73	22	55581	8	3	5	0	81
ASE_00277	RNaseP_bact_a links to Rfam database...	0.42	0.24	0.73	22	48175	8	3	5	0	69
ASE_00279	RNaseP_bact_a links to Rfam database...	0.42	0.23	0.79	23	53272	6	1	5	0	78
ASE_00285	RNaseP_bact_a links to Rfam database...	0.39	0.19	0.79	23	68977	6	1	5	0	99
ASE_00287	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	54917	6	1	5	0	80
ASE_00294	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.82	36	114437	8	1	7	0	135
ASE_00295	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.82	36	73876	8	1	7	0	95
ASE_00298	RNaseP_bact_a links to Rfam database...	0.40	0.20	0.79	23	67499	6	1	5	0	90
ASE_00318	RNaseP_bact_b links to Rfam database...	0.66	0.48	0.89	57	80136	13	1	6	6	61
ASE_00321	RNaseP_bact_b links to Rfam database...	0.66	0.51	0.87	45	54563	12	1	6	5	43
ASE_00335	RNaseP_bact_b links to Rfam database...	0.68	0.52	0.90	60	75399	12	1	6	5	56
ASE_00339	RNaseP_bact_a links to Rfam database...	0.48	0.29	0.81	34	80158	9	1	7	1	85
ASE_00340	RNaseP_bact_a links to Rfam database...	0.43	0.21	0.86	18	46035	3	0	3	0	67
ASE_00343	RNaseP_bact_a links to Rfam database...	0.31	0.16	0.60	18	83406	12	2	10	0	95
ASE_00367	RNaseP_bact_a links to Rfam database...	0.46	0.27	0.79	23	43042	6	1	5	0	63
ASE_00370	RNaseP_bact_a links to Rfam database...	0.45	0.26	0.76	22	41876	7	1	6	0	62
ASE_00372	RNaseP_bact_a links to Rfam database...	0.41	0.22	0.76	22	51974	7	1	6	0	78
ASE_00375	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.79	23	60349	6	1	5	0	87
ASE_00376	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.79	23	56924	6	1	5	0	82
ASE_00377	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.77	23	57600	7	2	5	0	84
ASE_00386	RNaseP_bact_a links to Rfam database...	0.44	0.24	0.79	23	50374	6	1	5	0	73
ASE_00393	RNaseP_bact_a links to Rfam database...	0.40	0.23	0.72	21	47866	8	1	7	0	72
ASE_00412	RNaseP_bact_a links to Rfam database...	0.39	0.21	0.73	22	58281	8	3	5	0	83
ASE_00413	RNaseP_bact_a links to Rfam database...	0.46	0.27	0.79	22	44523	6	1	5	0	59
ASE_00416	RNaseP_bact_a links to Rfam database...	0.47	0.28	0.80	35	77377	9	1	8	0	92
ASE_00417	RNaseP_arch links to Rfam database...	0.76	0.59	0.98	59	54555	1	0	1	0	41
ASE_00422	RNaseP_bact_a links to Rfam database...	0.40	0.19	0.86	18	46950	3	0	3	0	76
ASE_00427	RNaseP_nuc links to Rfam database...	0.55	0.30	1.00	14	40741	0	0	0	0	32
ASE_00428	RNaseP_bact_a links to Rfam database...	0.47	0.28	0.80	35	76592	9	1	8	0	90
ASE_00430	RNaseP_bact_a links to Rfam database...	0.41	0.21	0.83	20	46947	4	0	4	0	77
ASE_00434	RNaseP_bact_b links to Rfam database...	0.64	0.50	0.82	55	68198	17	1	11	5	55
ASE_00437	RNaseP_bact_a links to Rfam database...	0.30	0.17	0.55	23	79359	19	1	18	0	112
ASE_00451	RNaseP_bact_a links to Rfam database...	0.48	0.29	0.82	36	70832	8	1	7	0	89
ASE_00454	RNaseP_nuc links to Rfam database...	0.53	0.29	1.00	18	43347	0	0	0	0	45
CRW_00671	Intron_gpI links to Rfam database...	0.49	0.25	0.97	29	62805	1	0	1	0	88
CRW_00672	Intron_gpI links to Rfam database...	0.50	0.26	0.97	29	72360	1	0	1	0	82
CRW_00674	Intron_gpI links to Rfam database...	0.29	0.14	0.63	17	83409	10	6	4	0	107
CRW_00676	Intron_gpI links to Rfam database...	0.32	0.15	0.68	17	93503	13	0	8	5	98
RFA_00620	Telomerase-cil links to Rfam database...	0.88	0.77	1.00	30	21915	0	0	0	0	9
RFA_00816	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	23192	0	0	0	0	13
SRP_00103	Metazoa_SRP links to Rfam database...	0.77	0.62	0.97	63	45386	2	0	2	0	39
SRP_00117	Metazoa_SRP links to Rfam database...	0.77	0.60	0.98	61	45389	4	0	1	3	41
SRP_00144	Archaea_SRP links to Rfam database...	0.84	0.76	0.93	71	46589	9	0	5	4	23
SRP_00173	Bacteria_large_SRP links to Rfam database...	0.54	0.29	1.00	26	38200	1	0	0	1	64
SRP_00197	Archaea_SRP links to Rfam database...	0.83	0.72	0.96	73	49379	8	0	3	5	28
SRP_00198	Archaea_SRP links to Rfam database...	0.82	0.71	0.96	73	50964	8	0	3	5	30
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.55	0.30	1.00	26	36289	1	0	0	1	60
SRP_00267	Metazoa_SRP links to Rfam database...	0.80	0.65	0.98	62	44488	3	0	1	2	34
SRP_00276	Archaea_SRP links to Rfam database...	0.83	0.70	0.97	77	50642	3	0	2	1	33
SRP_00278	Archaea_SRP links to Rfam database...	0.77	0.65	0.91	68	45981	9	0	7	2	37
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.55	0.31	1.00	27	36288	0	0	0	0	61
SRP_00317	Metazoa_SRP links to Rfam database...	0.78	0.63	0.97	62	45086	3	0	2	1	36
SRP_00321	Archaea_SRP links to Rfam database...	0.80	0.67	0.96	72	47511	5	1	2	2	36
SRP_00322	Archaea_SRP links to Rfam database...	0.78	0.65	0.93	71	48440	7	0	5	2	38
SRP_00332	Archaea_SRP links to Rfam database...	0.84	0.72	0.97	76	50325	3	0	2	1	30
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.54	0.30	1.00	27	35484	0	0	0	0	64
TMR_00357	tmRNA links to Rfam database...	0.30	0.16	0.56	15	83001	12	3	9	0	77

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Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	1614
Total TN	4402260
Total FP	8930
Total FP CONTRA	1294
Total FP INCONS	7431
Total FP COMP	205
Total FN	6325

Total Scores
MCC	0.176
Average MCC ± 95% Confidence Intervals	0.175 ± 0.026
Sensitivity	0.203
Positive Predictive Value	0.156
Nr of predictions	78

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00017	RNaseP_nuc links to Rfam database...	0.02	0.03	0.02	2	50914	131	38	86	7	62
ASE_00083	RNaseP_bact_a links to Rfam database...	0.22	0.25	0.20	27	62347	108	12	95	1	83
ASE_00122	RNaseP_bact_a links to Rfam database...	0.27	0.30	0.24	26	43258	84	13	68	3	62
ASE_00185	RNaseP_bact_a links to Rfam database...	0.17	0.19	0.16	24	73382	134	14	116	4	104
ASE_00190	RNaseP_bact_b links to Rfam database...	0.24	0.28	0.21	25	45334	93	14	78	1	65
ASE_00191	RNaseP_arch links to Rfam database...	0.36	0.43	0.30	26	29559	67	15	46	6	35
ASE_00196	RNaseP_arch links to Rfam database...	0.49	0.57	0.42	43	31524	62	16	43	3	32
ASE_00221	RNaseP_bact_a links to Rfam database...	0.20	0.21	0.18	25	64484	112	10	101	1	92
ASE_00227	RNaseP_bact_a links to Rfam database...	0.28	0.31	0.25	41	78840	122	20	102	0	92
ASE_00228	RNaseP_bact_a links to Rfam database...	0.05	0.06	0.04	5	46858	109	17	91	1	81
ASE_00229	RNaseP_bact_a links to Rfam database...	0.12	0.14	0.11	12	42380	97	12	82	3	75
ASE_00231	RNaseP_bact_a links to Rfam database...	0.37	0.42	0.33	40	47773	84	17	65	2	56
ASE_00234	RNaseP_bact_a links to Rfam database...	0.25	0.27	0.23	35	75315	117	10	106	1	94
ASE_00238	RNaseP_bact_a links to Rfam database...	0.26	0.30	0.23	34	64111	119	18	98	3	80
ASE_00248	RNaseP_bact_a links to Rfam database...	0.13	0.15	0.12	17	62340	124	9	115	0	97
ASE_00250	RNaseP_bact_a links to Rfam database...	0.25	0.29	0.23	38	78835	135	17	113	5	93
ASE_00254	RNaseP_bact_a links to Rfam database...	0.15	0.16	0.14	13	36761	88	3	79	6	69
ASE_00255	RNaseP_bact_a links to Rfam database...	0.11	0.12	0.10	16	74530	146	16	129	1	114
ASE_00257	RNaseP_bact_a links to Rfam database...	0.37	0.42	0.33	41	50917	85	15	67	3	56
ASE_00267	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	45036	115	9	105	1	88
ASE_00270	RNaseP_bact_a links to Rfam database...	0.19	0.21	0.17	27	72232	132	14	117	1	101
ASE_00274	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	55487	126	12	112	2	103
ASE_00277	RNaseP_bact_a links to Rfam database...	0.10	0.12	0.08	11	48071	123	23	100	0	80
ASE_00279	RNaseP_bact_a links to Rfam database...	0.14	0.16	0.13	16	53177	109	16	92	1	85
ASE_00285	RNaseP_bact_a links to Rfam database...	0.34	0.36	0.31	44	68866	98	14	82	2	78
ASE_00287	RNaseP_bact_a links to Rfam database...	0.15	0.17	0.14	17	54824	107	14	91	2	86
ASE_00294	RNaseP_bact_a links to Rfam database...	0.12	0.13	0.12	23	114287	172	11	160	1	148
ASE_00295	RNaseP_bact_a links to Rfam database...	0.14	0.16	0.13	21	73761	140	19	119	2	110
ASE_00298	RNaseP_bact_a links to Rfam database...	0.09	0.10	0.08	11	67389	129	8	120	1	102
ASE_00318	RNaseP_bact_b links to Rfam database...	0.03	0.04	0.03	5	80039	156	21	135	0	113
ASE_00321	RNaseP_bact_b links to Rfam database...	0.11	0.14	0.09	12	54484	122	22	97	3	76
ASE_00335	RNaseP_bact_b links to Rfam database...	0.10	0.12	0.09	14	75304	151	22	126	3	102
ASE_00339	RNaseP_bact_a links to Rfam database...	0.25	0.29	0.22	34	80042	129	20	104	5	85
ASE_00340	RNaseP_bact_a links to Rfam database...	0.06	0.07	0.05	6	45943	110	13	94	3	79
ASE_00343	RNaseP_bact_a links to Rfam database...	0.14	0.17	0.12	19	83275	145	31	111	3	94
ASE_00367	RNaseP_bact_a links to Rfam database...	0.08	0.09	0.07	8	42960	110	10	93	7	78
ASE_00370	RNaseP_bact_a links to Rfam database...	0.03	0.04	0.03	3	41796	109	18	88	3	81
ASE_00372	RNaseP_bact_a links to Rfam database...	0.17	0.20	0.15	20	51871	113	19	93	1	80
ASE_00375	RNaseP_bact_a links to Rfam database...	0.12	0.14	0.11	15	60246	120	10	107	3	95
ASE_00376	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	56822	136	9	122	5	105
ASE_00377	RNaseP_bact_a links to Rfam database...	0.25	0.27	0.23	29	57505	98	10	86	2	78
ASE_00386	RNaseP_bact_a links to Rfam database...	0.14	0.16	0.13	15	50284	106	9	95	2	81
ASE_00393	RNaseP_bact_a links to Rfam database...	0.31	0.35	0.27	33	47773	90	18	71	1	60
ASE_00412	RNaseP_bact_a links to Rfam database...	0.15	0.17	0.14	18	58183	111	14	96	1	87
ASE_00413	RNaseP_bact_a links to Rfam database...	0.08	0.10	0.07	8	44438	108	19	86	3	73
ASE_00416	RNaseP_bact_a links to Rfam database...	0.39	0.43	0.35	54	77267	103	18	82	3	73
ASE_00417	RNaseP_arch links to Rfam database...	0.32	0.36	0.28	36	54486	98	18	75	5	64
ASE_00422	RNaseP_bact_a links to Rfam database...	0.28	0.31	0.25	29	46856	87	9	77	1	65
ASE_00427	RNaseP_nuc links to Rfam database...	0.06	0.09	0.04	4	40651	105	35	65	5	42
ASE_00428	RNaseP_bact_a links to Rfam database...	0.24	0.26	0.22	33	76483	121	13	107	1	92
ASE_00430	RNaseP_bact_a links to Rfam database...	0.16	0.18	0.14	17	46852	102	10	92	0	80
ASE_00434	RNaseP_bact_b links to Rfam database...	0.29	0.34	0.25	37	68116	122	20	92	10	73
ASE_00437	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	79238	164	12	151	1	135
ASE_00451	RNaseP_bact_a links to Rfam database...	0.20	0.22	0.19	27	70731	118	8	110	0	98
ASE_00454	RNaseP_nuc links to Rfam database...	0.24	0.32	0.19	20	43260	103	28	57	18	43
CRW_00671	Intron_gpI links to Rfam database...	0.18	0.21	0.16	24	62682	130	23	106	1	93
CRW_00672	Intron_gpI links to Rfam database...	0.36	0.43	0.31	48	72233	114	35	74	5	63
CRW_00674	Intron_gpI links to Rfam database...	0.16	0.19	0.14	23	83274	142	19	120	3	101
CRW_00676	Intron_gpI links to Rfam database...	0.11	0.14	0.09	16	93347	169	29	136	4	99
RFA_00620	Telomerase-cil links to Rfam database...	0.16	0.23	0.11	9	21864	80	29	43	8	30
RFA_00816	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	23133	89	30	57	2	41
SRP_00103	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	45319	132	14	118	0	102
SRP_00117	Metazoa_SRP links to Rfam database...	0.20	0.23	0.18	23	45322	106	9	97	0	79
SRP_00144	Archaea_SRP links to Rfam database...	0.05	0.06	0.05	6	46538	122	17	104	1	88
SRP_00173	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	38104	124	13	109	2	90
SRP_00197	Archaea_SRP links to Rfam database...	0.12	0.14	0.11	14	49324	117	16	101	0	87
SRP_00198	Archaea_SRP links to Rfam database...	0.07	0.08	0.06	8	50903	129	15	114	0	95
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.21	0.24	0.18	21	36200	97	19	75	3	65
SRP_00267	Metazoa_SRP links to Rfam database...	0.04	0.05	0.04	5	44424	122	15	107	0	91
SRP_00276	Archaea_SRP links to Rfam database...	0.19	0.22	0.18	24	50585	112	10	102	0	86
SRP_00278	Archaea_SRP links to Rfam database...	0.33	0.36	0.30	38	45928	90	14	76	0	67
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.14	0.17	0.12	15	36189	112	18	93	1	73
SRP_00317	Metazoa_SRP links to Rfam database...	0.14	0.16	0.12	16	45018	116	16	100	0	82
SRP_00321	Archaea_SRP links to Rfam database...	0.44	0.49	0.40	53	47453	81	16	64	1	55
SRP_00322	Archaea_SRP links to Rfam database...	0.22	0.25	0.21	27	48385	105	8	96	1	82
SRP_00332	Archaea_SRP links to Rfam database...	0.12	0.14	0.11	15	50269	120	8	111	1	91
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.42	0.46	0.38	42	35400	70	15	54	1	49
TMR_00357	tmRNA links to Rfam database...	0.26	0.34	0.19	31	82869	146	44	84	18	61

^top

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 RNAalifold(seed) - scored higher in this pairwise comparison

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

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

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

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