CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Vsfold5		CentroidFold
MCC	0.534	>	0.482
Average MCC ± 95% Confidence Intervals	0.598 ± 0.089	>	0.548 ± 0.084
Sensitivity	0.505	>	0.430
Positive Predictive Value	0.572	>	0.548
Total TP	595	>	507
Total TN	158465	<	158581
Total FP	457	>	427
Total FP CONTRA	74	>	53
Total FP INCONS	372	>	365
Total FP COMP	11	>	9
Total FN	583	<	671
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	595
Total TN	158465
Total FP	457
Total FP CONTRA	74
Total FP INCONS	372
Total FP COMP	11
Total FN	583

Total Scores
MCC	0.534
Average MCC ± 95% Confidence Intervals	0.598 ± 0.089
Sensitivity	0.505
Positive Predictive Value	0.572
Nr of predictions	53

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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_00005	Tymo_tRNA-like links to Rfam database...	0.78	0.79	0.79	11	932	3	1	2	0	3
PDB_00018	-	0.68	0.55	0.85	11	1022	2	2	0	0	9
PDB_00020	-	0.80	0.70	0.93	14	765	1	0	1	0	6
PDB_00041	-	0.96	0.92	1.00	11	619	0	0	0	0	1
PDB_00053	-	1.00	1.00	1.00	11	424	0	0	0	0	0
PDB_00056	-	0.90	0.81	1.00	13	617	0	0	0	0	3
PDB_00123	-	0.35	0.33	0.38	12	4154	20	0	20	0	24
PDB_00124	-	0.86	0.90	0.82	9	485	2	2	0	0	1
PDB_00128	-	0.61	0.57	0.67	8	484	4	0	4	0	6
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.96	1.00	0.92	11	549	1	1	0	0	0
PDB_00243	-	0.96	0.92	1.00	11	619	0	0	0	0	1
PDB_00352	-	0.72	0.68	0.76	13	1208	4	3	1	0	6
PDB_00370	-	0.10	0.12	0.08	3	15187	35	16	19	0	22
PDB_00447	-	0.95	0.91	1.00	40	7100	0	0	0	0	4
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00713	-	0.69	0.62	0.76	13	1999	4	0	4	0	8
PDB_00716	HDV_ribozyme links to Rfam database...	0.17	0.17	0.18	4	2679	19	0	18	1	19
PDB_00804	-	0.19	0.20	0.18	10	15344	48	6	40	2	40
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
PDB_00829	Purine links to Rfam database...	0.83	0.79	0.86	19	2256	3	2	1	0	5
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.54	0.44	0.67	18	4726	9	0	9	0	23
PDB_00857	-	1.00	1.00	1.00	15	1066	0	0	0	0	0
PDB_00874	-	-0.02	0.00	0.00	0	932	14	0	14	0	20
PDB_00886	-	0.64	0.60	0.69	24	4151	11	0	11	0	16
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.90	0.90	0.90	19	2464	3	0	2	1	2
PDB_01020	Purine links to Rfam database...	0.82	0.78	0.86	18	2257	4	2	1	1	5
PDB_01040	-	0.30	0.30	0.33	6	1110	12	0	12	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.43	0.37	0.50	20	12680	20	0	20	0	34
PDB_01073	SAM links to Rfam database...	0.56	0.47	0.67	16	4347	9	1	7	1	18
PDB_01092	glmS links to Rfam database...	0.73	0.69	0.77	36	10106	12	2	9	1	16
PDB_01194	-	0.73	0.60	0.90	9	486	1	1	0	0	6
PDB_01201	-	0.79	0.64	1.00	14	1114	0	0	0	0	8
PDB_01203	-	0.73	0.63	0.86	12	1162	2	2	0	0	7
PDB_01250	-	0.16	0.15	0.18	6	12056	30	3	25	2	35
PDB_01260	-	0.41	0.36	0.47	9	1811	10	0	10	0	16
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.90	0.87	0.93	13	889	1	1	0	0	2
PDB_01309	-	-0.01	0.00	0.00	0	9125	55	12	43	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	4073	22	0	22	0	28
RFA_00636	HDV_ribozyme links to Rfam database...	0.58	0.57	0.59	16	3978	11	1	10	0	12
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

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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	507
Total TN	158581
Total FP	427
Total FP CONTRA	53
Total FP INCONS	365
Total FP COMP	9
Total FN	671

Total Scores
MCC	0.482
Average MCC ± 95% Confidence Intervals	0.548 ± 0.084
Sensitivity	0.430
Positive Predictive Value	0.548
Nr of predictions	53

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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
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00018	-	0.20	0.20	0.22	4	1017	14	2	12	0	16
PDB_00020	-	0.38	0.35	0.44	7	764	9	0	9	0	13
PDB_00041	-	0.70	0.50	1.00	6	624	0	0	0	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	0	5
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	-0.01	0.00	0.00	0	4151	35	0	35	0	36
PDB_00124	-	-0.02	0.00	0.00	0	488	8	2	6	0	10
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.67	0.45	1.00	5	556	0	0	0	0	6
PDB_00243	-	0.63	0.58	0.70	7	620	3	0	3	0	5
PDB_00352	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00370	-	0.00	0.00	0.00	0	15219	6	0	6	0	25
PDB_00447	-	0.59	0.41	0.86	18	7119	3	3	0	0	26
PDB_00571	tRNA links to Rfam database...	0.77	0.64	0.94	16	3304	1	1	0	0	9
PDB_00713	-	0.54	0.48	0.63	10	2000	6	1	5	0	11
PDB_00716	HDV_ribozyme links to Rfam database...	0.33	0.30	0.37	7	2682	13	0	12	1	16
PDB_00804	-	0.22	0.24	0.21	12	15342	46	10	36	0	38
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.44	0.39	0.50	16	4721	16	0	16	0	25
PDB_00857	-	0.77	0.60	1.00	9	1072	0	0	0	0	6
PDB_00874	-	-0.02	0.00	0.00	0	929	17	0	17	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.46	0.52	0.41	11	2458	16	5	11	0	10
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.30	0.30	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.38	0.28	0.52	15	12691	14	0	14	0	39
PDB_01073	SAM links to Rfam database...	0.86	0.74	1.00	25	4346	1	0	0	1	9
PDB_01092	glmS links to Rfam database...	0.71	0.63	0.80	33	10112	10	1	7	2	19
PDB_01194	-	-0.02	0.00	0.00	0	487	9	0	9	0	15
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.72	0.68	0.76	13	1159	4	3	1	0	6
PDB_01250	-	0.18	0.15	0.22	6	12063	21	5	16	0	35
PDB_01260	-	0.64	0.48	0.86	12	1816	2	0	2	0	13
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.74	0.67	0.83	10	891	2	1	1	0	5
PDB_01309	-	-0.01	0.00	0.00	0	9118	62	9	53	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.67	0.61	0.74	17	4072	6	1	5	0	11
RFA_00636	HDV_ribozyme links to Rfam database...	0.64	0.64	0.64	18	3977	10	4	6	0	10
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...	0.45	0.44	0.47	8	1874	9	1	8	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.64	0.50	0.82	9	2005	4	0	2	2	9
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	3	1	0	2	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	0	2	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...	0.43	0.38	0.50	6	2133	6	0	6	0	10

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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 Vsfold5 - scored higher in this pairwise comparison

1. Total counts & total scores for Vsfold5

2. Individual counts for Vsfold5 [ 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 ]