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		CRWrnafold
MCC	0.534	>	0.374
Average MCC ± 95% Confidence Intervals	0.598 ± 0.089	>	0.450 ± 0.090
Sensitivity	0.505	>	0.351
Positive Predictive Value	0.572	>	0.407
Total TP	595	>	414
Total TN	158465	<	158490
Total FP	457	<	618
Total FP CONTRA	74	<	81
Total FP INCONS	372	<	521
Total FP COMP	11	<	16
Total FN	583	<	764
P-value	3.56938820447e-08

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Performance plots

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

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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 CRWrnafold - scored lower in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	414
Total TN	158490
Total FP	618
Total FP CONTRA	81
Total FP INCONS	521
Total FP COMP	16
Total FN	764

Total Scores
MCC	0.374
Average MCC ± 95% Confidence Intervals	0.450 ± 0.090
Sensitivity	0.351
Positive Predictive Value	0.407
Nr of predictions	53

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2. Individual counts for CRWrnafold [ 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	-	0.21	0.20	0.25	4	1019	12	2	10	0	16
PDB_00020	-	0.42	0.35	0.54	7	767	6	0	6	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	4155	31	0	31	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	-	0.66	0.63	0.71	5	371	2	0	2	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.68	0.55	0.86	6	554	1	1	0	0	5
PDB_00243	-	0.76	0.58	1.00	7	623	0	0	0	0	5
PDB_00352	-	0.39	0.37	0.44	7	1209	9	0	9	0	12
PDB_00370	-	0.00	0.00	0.00	0	15179	46	13	33	0	25
PDB_00447	-	-0.01	0.00	0.00	0	7110	30	6	24	0	44
PDB_00571	tRNA links to Rfam database...	0.85	0.76	0.95	19	3301	1	1	0	0	6
PDB_00713	-	-0.01	0.00	0.00	0	1998	19	1	17	1	21
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	22	0	21	1	23
PDB_00804	-	0.00	0.00	0.00	0	15344	56	10	46	0	50
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	-	0.42	0.39	0.47	16	4719	18	4	14	0	25
PDB_00857	-	0.77	0.60	1.00	9	1072	0	0	0	0	6
PDB_00874	-	0.10	0.10	0.13	2	931	13	2	11	0	18
PDB_00886	-	-0.01	0.00	0.00	0	4152	34	0	34	0	40
PDB_00918	-	0.56	0.43	0.75	3	321	1	1	0	0	4
PDB_01009	tRNA links to Rfam database...	0.90	0.90	0.90	19	2464	4	0	2	2	2
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.31	0.30	0.35	6	1111	11	0	11	0	14
PDB_01059	-	0.56	0.43	0.75	3	227	1	1	0	0	4
PDB_01070	-	0.27	0.26	0.29	14	12672	34	0	34	0	40
PDB_01073	SAM links to Rfam database...	0.52	0.47	0.59	16	4344	12	1	10	1	18
PDB_01092	glmS links to Rfam database...	0.68	0.62	0.76	32	10111	12	1	9	2	20
PDB_01194	-	0.44	0.33	0.63	5	488	3	1	2	0	10
PDB_01201	-	0.82	0.68	1.00	15	1113	0	0	0	0	7
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01250	-	0.15	0.15	0.16	6	12053	31	4	27	0	35
PDB_01260	-	0.44	0.36	0.56	9	1814	7	0	7	0	16
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	-0.01	0.00	0.00	0	894	9	2	7	0	15
PDB_01309	-	-0.01	0.00	0.00	0	9122	58	7	51	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.37	0.36	0.38	10	4069	19	0	16	3	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.51	0.50	0.52	14	3978	13	3	10	0	14
RFA_00767	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	3	3	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.47	0.44	0.50	8	1875	8	1	7	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1934	9	4	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	2002	17	1	13	3	18
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	3	3	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2000	18	2	14	2	16
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	1	7	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 CRWrnafold - scored lower in this pairwise comparison

1. Total counts & total scores for CRWrnafold

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