CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	PPfold(seed)		Vsfold5
MCC	0.635	>	0.233
Average MCC ± 95% Confidence Intervals	0.464 ± 0.097	>	0.315 ± 0.079
Sensitivity	0.511	>	0.221
Positive Predictive Value	0.790	>	0.250
Total TP	1350	>	585
Total TN	1044478	>	1043848
Total FP	501	<	1871
Total FP CONTRA	54	<	277
Total FP INCONS	304	<	1476
Total FP COMP	143	>	118
Total FN	1294	<	2059
P-value	3.56938820447e-08

^top

Performance plots

Comparison of performance of PPfold(seed) and Vsfold5. 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 PPfold(seed) and Vsfold5).
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 PPfold(seed) and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(seed) and Vsfold5. 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 PPfold(seed) and Vsfold5).

^top

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

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

Total Base Pair Counts
Total TP	1350
Total TN	1044478
Total FP	501
Total FP CONTRA	54
Total FP INCONS	304
Total FP COMP	143
Total FN	1294

Total Scores
MCC	0.635
Average MCC ± 95% Confidence Intervals	0.464 ± 0.097
Sensitivity	0.511
Positive Predictive Value	0.790
Nr of predictions	62

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_01001	tRNA links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	18
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	1	0	0	1	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	1	0	0	1	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00626	rne5 links to Rfam database...	0.94	0.89	1.00	77	56539	1	0	0	1	10
RFA_00627	rne5 links to Rfam database...	0.95	0.91	1.00	79	56874	4	0	0	4	8
RFA_00628	rne5 links to Rfam database...	0.95	0.91	1.00	78	57213	2	0	0	2	8
RFA_00630	rne5 links to Rfam database...	0.91	0.85	0.97	74	56877	5	0	2	3	13
RFA_00654	Vimentin3 links to Rfam database...	0.23	0.17	0.33	3	2406	6	0	6	0	15
RFA_00658	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	1126	1	0	0	1	12
RFA_00664	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	988	1	0	0	1	12
RFA_00708	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	1033	1	0	0	1	12
RFA_00749	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00764	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00765	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00767	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	1	1	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
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...	0.94	0.88	1.00	36	25164	2	0	0	2	5
RFA_00816	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	23183	2	0	0	2	4
RFA_00817	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	21908	1	0	0	1	4
RFA_00818	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	20265	2	0	0	2	5
RFA_00819	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	27929	2	0	0	2	4
SPR_00020	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	20
SPR_00137	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00277	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00394	tRNA links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	21
SPR_00402	tRNA links to Rfam database...	0.00	0.00	0.00	0	2556	0	0	0	0	21
SPR_00721	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00816	tRNA links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	20
SPR_01157	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	21
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	33
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5778	0	0	0	0	34
SRP_00079	Plant_SRP links to Rfam database...	0.74	0.69	0.79	61	41828	28	0	16	12	27
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00099	Plant_SRP links to Rfam database...	0.60	0.59	0.62	56	44760	40	2	32	6	39
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	34
SRP_00124	Metazoa_SRP links to Rfam database...	0.71	0.66	0.76	56	37054	27	3	15	9	29
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	5995	0	0	0	0	29
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	41
SRP_00182	Plant_SRP links to Rfam database...	0.85	0.78	0.92	79	45970	17	0	7	10	22
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00241	Plant_SRP links to Rfam database...	0.53	0.52	0.54	43	45977	49	9	27	13	39
SRP_00252	Metazoa_SRP links to Rfam database...	0.64	0.63	0.64	56	49054	42	5	26	11	33
SRP_00253	Metazoa_SRP links to Rfam database...	0.64	0.62	0.66	56	49370	40	5	24	11	34
SRP_00257	Metazoa_SRP links to Rfam database...	0.51	0.44	0.59	48	50959	36	5	28	3	60
SRP_00260	Metazoa_SRP links to Rfam database...	0.56	0.51	0.61	51	47811	39	5	28	6	49
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6786	0	0	0	0	40
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	38
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3741	0	0	0	0	30
SRP_00328	Metazoa_SRP links to Rfam database...	0.61	0.56	0.67	48	39549	29	5	19	5	37
SRP_00329	Metazoa_SRP links to Rfam database...	0.72	0.67	0.78	57	39830	26	2	14	10	28
SRP_00331	Metazoa_SRP links to Rfam database...	0.63	0.59	0.69	51	37601	31	2	21	8	36
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36
SRP_00340	Metazoa_SRP links to Rfam database...	0.54	0.50	0.59	41	41258	42	5	24	13	41
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	31
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5356	0	0	0	0	36

^top

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	585
Total TN	1043848
Total FP	1871
Total FP CONTRA	277
Total FP INCONS	1476
Total FP COMP	118
Total FN	2059

Total Scores
MCC	0.233
Average MCC ± 95% Confidence Intervals	0.315 ± 0.079
Sensitivity	0.221
Positive Predictive Value	0.250
Nr of predictions	62

^top

2. Individual counts for Vsfold5 [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_01001	tRNA links to Rfam database...	-0.01	0.00	0.00	0	2130	15	3	12	0	18
RFA_00390	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	2	0	0	2	2
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.93	0.93	14	1470	4	0	1	3	1
RFA_00433	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00626	rne5 links to Rfam database...	0.31	0.31	0.32	27	56531	62	15	43	4	60
RFA_00627	rne5 links to Rfam database...	0.26	0.26	0.26	23	56863	69	16	51	2	64
RFA_00628	rne5 links to Rfam database...	0.34	0.35	0.34	30	57202	66	13	46	7	56
RFA_00630	rne5 links to Rfam database...	0.27	0.29	0.26	25	56857	78	13	58	7	62
RFA_00654	Vimentin3 links to Rfam database...	0.54	0.44	0.67	8	2403	5	1	3	1	10
RFA_00658	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	5	0	3	2	10
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00708	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1027	8	0	8	0	14
RFA_00749	s2m links to Rfam database...	0.51	0.42	0.63	5	895	4	1	2	1	7
RFA_00764	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00765	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00767	Corona_pk3 links to Rfam database...	0.21	0.22	0.22	4	1873	14	2	12	0	14
RFA_00768	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1875	16	1	15	0	18
RFA_00769	Corona_pk3 links to Rfam database...	0.50	0.50	0.50	9	1935	9	4	5	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	2003	3	3	0	0	8
RFA_00773	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1936	19	1	16	2	18
RFA_00779	Corona_pk3 links to Rfam database...	0.69	0.61	0.79	11	1939	3	3	0	0	7
RFA_00808	RydC links to Rfam database...	1.00	1.00	1.00	16	2000	0	0	0	0	0
RFA_00809	RydC links to Rfam database...	0.45	0.44	0.47	7	2130	8	1	7	0	9
RFA_00814	R2_retro_el links to Rfam database...	0.31	0.34	0.29	14	25151	46	10	25	11	27
RFA_00816	R2_retro_el links to Rfam database...	0.31	0.32	0.30	13	23177	38	12	18	8	28
RFA_00817	R2_retro_el links to Rfam database...	0.32	0.34	0.30	14	21898	35	10	23	2	27
RFA_00818	R2_retro_el links to Rfam database...	0.19	0.20	0.19	8	20258	41	8	27	6	33
RFA_00819	R2_retro_el links to Rfam database...	0.27	0.27	0.28	11	27926	53	6	23	24	30
SPR_00020	tRNA links to Rfam database...	0.76	0.80	0.73	16	2679	7	4	2	1	4
SPR_00137	tRNA links to Rfam database...	0.83	0.81	0.85	17	2906	8	0	3	5	4
SPR_00277	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00394	tRNA links to Rfam database...	0.52	0.52	0.52	11	3634	14	5	5	4	10
SPR_00402	tRNA links to Rfam database...	0.71	0.76	0.67	16	2532	9	4	4	1	5
SPR_00721	tRNA links to Rfam database...	0.62	0.67	0.58	14	2902	10	2	8	0	7
SPR_00816	tRNA links to Rfam database...	0.32	0.35	0.30	7	3463	19	4	12	3	13
SPR_01157	tRNA links to Rfam database...	0.84	0.86	0.82	18	2753	4	4	0	0	3
SRP_00020	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5538	27	2	25	0	33
SRP_00058	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5749	29	5	24	0	34
SRP_00079	Plant_SRP links to Rfam database...	0.14	0.14	0.15	12	41823	72	4	66	2	76
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.17	0.15	0.20	5	5435	20	3	17	0	29
SRP_00099	Plant_SRP links to Rfam database...	0.07	0.06	0.08	6	44770	74	8	66	0	89
SRP_00105	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5534	31	3	28	0	34
SRP_00124	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	37128	0	0	0	0	85
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.22	0.21	0.25	6	5971	21	5	13	3	23
SRP_00141	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	6299	29	1	28	0	41
SRP_00182	Plant_SRP links to Rfam database...	0.16	0.16	0.17	16	45964	76	7	69	0	85
SRP_00231	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5433	27	3	24	0	34
SRP_00241	Plant_SRP links to Rfam database...	0.07	0.07	0.07	6	45966	85	13	71	1	76
SRP_00252	Metazoa_SRP links to Rfam database...	0.18	0.18	0.17	16	49049	79	7	69	3	73
SRP_00253	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	49361	96	14	80	2	90
SRP_00257	Metazoa_SRP links to Rfam database...	0.30	0.27	0.34	29	50955	58	2	54	2	79
SRP_00260	Metazoa_SRP links to Rfam database...	0.12	0.11	0.13	11	47812	72	7	65	0	89
SRP_00273	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	6754	32	2	30	0	40
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.28	0.26	0.30	10	6870	23	2	21	0	28
SRP_00285	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3719	22	2	20	0	30
SRP_00328	Metazoa_SRP links to Rfam database...	0.19	0.18	0.21	15	39548	60	10	48	2	70
SRP_00329	Metazoa_SRP links to Rfam database...	0.23	0.22	0.25	19	39826	58	15	43	0	66
SRP_00331	Metazoa_SRP links to Rfam database...	0.19	0.18	0.21	16	37597	62	7	55	0	71
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36
SRP_00340	Metazoa_SRP links to Rfam database...	0.11	0.11	0.11	9	41246	75	9	64	2	73
SRP_00341	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4725	28	0	28	0	31
SRP_00357	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	5330	26	0	26	0	36

^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 PPfold(seed) - scored higher in this pairwise comparison

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

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

Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ download as .csv ]