CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	TurboFold(seed)		RNAalifold(seed)
MCC	0.788	>	0.688
Average MCC ± 95% Confidence Intervals	0.780 ± 0.060	>	0.639 ± 0.072
Sensitivity	0.760	>	0.533
Positive Predictive Value	0.819	<	0.888
Total TP	1565	>	1099
Total TN	893700	<	894375
Total FP	540	>	208
Total FP CONTRA	62	>	14
Total FP INCONS	285	>	124
Total FP COMP	193	>	70
Total FN	495	<	961
P-value	3.56938820447e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	1565
Total TN	893700
Total FP	540
Total FP CONTRA	62
Total FP INCONS	285
Total FP COMP	193
Total FN	495

Total Scores
MCC	0.788
Average MCC ± 95% Confidence Intervals	0.780 ± 0.060
Sensitivity	0.760
Positive Predictive Value	0.819
Nr of predictions	50

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00210	RNaseP_arch links to Rfam database...	0.71	0.68	0.75	44	27202	16	4	11	1	21
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	11	0	0	11	0
RFA_00626	rne5 links to Rfam database...	0.90	0.85	0.95	74	56538	17	0	4	13	13
RFA_00627	rne5 links to Rfam database...	0.85	0.82	0.89	71	56873	23	0	9	14	16
RFA_00628	rne5 links to Rfam database...	0.92	0.90	0.95	77	57210	17	0	4	13	9
RFA_00630	rne5 links to Rfam database...	0.83	0.79	0.87	69	56874	22	0	10	12	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00654	Vimentin3 links to Rfam database...	0.44	0.33	0.60	6	2405	5	1	3	1	12
RFA_00658	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	5	0	3	2	7
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.67	0.64	0.69	9	4265	18	1	3	14	5
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	3	0	3	0	10
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	5	0	2	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	2	1	0	1	8
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	0	1	0	8
RFA_00805	RNAIII links to Rfam database...	0.87	0.82	0.93	123	133254	13	0	9	4	27
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.38	0.38	0.40	6	2130	9	1	8	0	10
RFA_00814	R2_retro_el links to Rfam database...	0.92	0.85	1.00	35	25165	13	0	0	13	6
RFA_00816	R2_retro_el links to Rfam database...	1.00	1.00	1.00	41	23179	14	0	0	14	0
RFA_00817	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	21908	7	0	0	7	4
RFA_00818	R2_retro_el links to Rfam database...	0.85	0.80	0.89	33	20264	11	1	3	7	8
RFA_00819	R2_retro_el links to Rfam database...	0.98	0.95	1.00	39	27927	27	0	0	27	2
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.88	0.88	0.88	30	5426	4	1	3	0	4
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.61	0.66	0.58	19	5962	18	3	11	4	10
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.75	0.84	0.68	21	4155	10	4	6	0	4
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5216	3	1	2	0	2
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.90	0.92	0.89	33	6866	4	1	3	0	3
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.91	0.91	0.91	31	5426	3	1	2	0	3
SRP_00241	Plant_SRP links to Rfam database...	0.56	0.59	0.54	48	45967	43	12	29	2	34
SRP_00257	Metazoa_SRP links to Rfam database...	0.78	0.72	0.85	78	50948	16	4	10	2	30
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.95	0.93	0.97	28	3712	1	0	1	0	2
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.76	0.74	0.77	65	36231	20	2	17	1	23
SRP_00328	Metazoa_SRP links to Rfam database...	0.69	0.67	0.70	57	39540	27	5	19	3	28
SRP_00329	Metazoa_SRP links to Rfam database...	0.65	0.64	0.67	54	39822	30	3	24	3	31
SRP_00331	Metazoa_SRP links to Rfam database...	0.67	0.66	0.68	57	37591	29	3	24	2	30
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.94	0.94	0.94	34	5424	2	0	2	0	2
SRP_00340	Metazoa_SRP links to Rfam database...	0.61	0.61	0.61	50	41246	38	6	26	6	32
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5319	3	1	2	0	2
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	33	6750	3	1	2	0	2

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

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

Total Base Pair Counts
Total TP	1099
Total TN	894375
Total FP	208
Total FP CONTRA	14
Total FP INCONS	124
Total FP COMP	70
Total FN	961

Total Scores
MCC	0.688
Average MCC ± 95% Confidence Intervals	0.639 ± 0.072
Sensitivity	0.533
Positive Predictive Value	0.888
Nr of predictions	50

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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_00210	RNaseP_arch links to Rfam database...	0.68	0.55	0.84	36	27218	9	0	7	2	29
PDB_00012	mir-TAR links to Rfam database...	0.65	0.43	1.00	3	403	0	0	0	0	4
RFA_00390	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1472	1	0	0	1	2
RFA_00433	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00587	Y_RNA links to Rfam database...	0.68	0.47	1.00	7	4844	0	0	0	0	8
RFA_00626	rne5 links to Rfam database...	0.97	0.94	1.00	82	56534	6	0	0	6	5
RFA_00627	rne5 links to Rfam database...	0.96	0.93	1.00	81	56872	7	0	0	7	6
RFA_00628	rne5 links to Rfam database...	0.97	0.94	1.00	81	57210	6	0	0	6	5
RFA_00630	rne5 links to Rfam database...	0.92	0.87	0.96	76	56874	12	0	3	9	11
RFA_00636	HDV_ribozyme links to Rfam database...	0.49	0.32	0.75	9	3993	3	2	1	0	19
RFA_00654	Vimentin3 links to Rfam database...	0.52	0.44	0.62	8	2402	5	0	5	0	10
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	4278	0	0	0	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00767	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	0	3	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	0	3	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	2003	3	0	3	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	0	3	0	8
RFA_00805	RNAIII links to Rfam database...	0.50	0.37	0.69	55	133306	25	0	25	0	95
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.50	0.38	0.67	6	2136	3	0	3	0	10
RFA_00814	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	25172	0	0	0	0	13
RFA_00816	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	23192	0	0	0	0	13
RFA_00817	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	21917	0	0	0	0	13
RFA_00818	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	20273	0	0	0	0	13
RFA_00819	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	27938	0	0	0	0	13
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	5451	0	0	0	0	25
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.70	0.62	0.78	18	5972	9	0	5	4	11
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.60	0.36	1.00	9	4177	0	0	0	0	16
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	5244	0	0	0	0	27
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	6894	0	0	0	0	27
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	5451	0	0	0	0	25
SRP_00241	Plant_SRP links to Rfam database...	0.59	0.48	0.72	39	46002	22	4	11	7	43
SRP_00257	Metazoa_SRP links to Rfam database...	0.55	0.40	0.77	43	50984	14	4	9	1	65
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.55	0.30	1.00	9	3732	0	0	0	0	21
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.55	0.31	1.00	27	36288	0	0	0	0	61
SRP_00328	Metazoa_SRP links to Rfam database...	0.64	0.48	0.85	41	39573	11	1	6	4	44
SRP_00329	Metazoa_SRP links to Rfam database...	0.66	0.51	0.86	43	39853	14	0	7	7	42
SRP_00331	Metazoa_SRP links to Rfam database...	0.58	0.47	0.72	41	37618	21	1	15	5	46
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	5451	0	0	0	0	27
SRP_00340	Metazoa_SRP links to Rfam database...	0.60	0.46	0.78	38	41279	20	2	9	9	44
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.50	0.25	1.00	9	5347	0	0	0	0	27
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.51	0.26	1.00	9	6777	0	0	0	0	26

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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 TurboFold(seed) - scored higher in this pairwise comparison

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

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

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

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

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