CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Pknots		Vsfold5
MCC	0.697	>	0.597
Average MCC ± 95% Confidence Intervals	0.757 ± 0.084	>	0.634 ± 0.090
Sensitivity	0.668	>	0.550
Positive Predictive Value	0.733	>	0.657
Total TP	583	>	480
Total TN	76803	<	76867
Total FP	237	<	257
Total FP CONTRA	31	<	35
Total FP INCONS	181	<	216
Total FP COMP	25	>	6
Total FN	290	<	393
P-value	3.56938820447e-08

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Performance plots

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

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Performance of Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

Total Base Pair Counts
Total TP	583
Total TN	76803
Total FP	237
Total FP CONTRA	31
Total FP INCONS	181
Total FP COMP	25
Total FN	290

Total Scores
MCC	0.697
Average MCC ± 95% Confidence Intervals	0.757 ± 0.084
Sensitivity	0.668
Positive Predictive Value	0.733
Nr of predictions	46

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2. Individual counts for Pknots [ 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...	1.00	1.00	1.00	14	932	0	0	0	0	0
PDB_00018	-	0.68	0.55	0.85	11	1022	2	2	0	0	9
PDB_00020	-	0.77	0.65	0.93	13	766	1	0	1	0	7
PDB_00041	-	1.00	1.00	1.00	12	618	0	0	0	0	0
PDB_00053	-	1.00	1.00	1.00	11	424	0	0	0	0	0
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	-0.01	0.00	0.00	0	4153	33	0	33	0	36
PDB_00124	-	0.86	0.90	0.82	9	485	2	2	0	0	1
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.94	1.00	0.89	8	369	1	1	0	0	0
PDB_00138	-	0.94	1.00	0.89	8	369	1	1	0	0	0
PDB_00209	-	0.96	1.00	0.92	11	549	1	1	0	0	0
PDB_00243	-	1.00	1.00	1.00	12	618	0	0	0	0	0
PDB_00352	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00713	-	0.45	0.43	0.47	9	1997	10	0	10	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	0.69	0.70	0.70	16	2678	8	0	7	1	7
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	2	0	0	2	7
PDB_00829	Purine links to Rfam database...	0.60	0.46	0.79	11	2264	5	0	3	2	13
PDB_00842	-	1.00	1.00	1.00	8	370	0	0	0	0	0
PDB_00851	-	0.44	0.39	0.50	16	4721	16	0	16	0	25
PDB_00857	-	1.00	1.00	1.00	15	1066	0	0	0	0	0
PDB_00874	-	-0.02	0.00	0.00	0	930	16	0	16	0	20
PDB_00886	-	0.37	0.35	0.41	14	4152	20	0	20	0	26
PDB_00918	-	0.93	1.00	0.88	7	317	1	1	0	0	0
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	3	0	0	3	6
PDB_01040	-	0.30	0.30	0.33	6	1110	12	0	12	0	14
PDB_01059	-	0.93	1.00	0.88	7	223	1	1	0	0	0
PDB_01073	SAM links to Rfam database...	0.51	0.47	0.55	16	4342	14	2	11	1	18
PDB_01194	-	0.77	0.60	1.00	9	487	0	0	0	0	6
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.95	0.95	0.95	18	1157	1	1	0	0	1
PDB_01260	-	0.65	0.64	0.67	16	1806	8	1	7	0	9
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.84	0.87	0.81	13	887	3	1	2	0	2
RFA_00632	HDV_ribozyme links to Rfam database...	0.40	0.43	0.39	12	4064	19	4	15	0	16
RFA_00636	HDV_ribozyme links to Rfam database...	0.80	0.86	0.75	24	3973	8	6	2	0	4
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	4	0	0	4	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	3	0	0	3	0
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...	0.97	0.94	1.00	17	1999	3	0	0	3	1
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	4	1	0	3	0
RFA_00779	Corona_pk3 links to Rfam database...	0.83	0.83	0.83	15	1935	4	1	2	1	3
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...	0.79	0.81	0.76	13	2128	4	0	4	0	3

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Performance of Vsfold5 - scored lower in this pairwise comparison

1. Total counts & total scores for Vsfold5

Total Base Pair Counts
Total TP	480
Total TN	76867
Total FP	257
Total FP CONTRA	35
Total FP INCONS	216
Total FP COMP	6
Total FN	393

Total Scores
MCC	0.597
Average MCC ± 95% Confidence Intervals	0.634 ± 0.090
Sensitivity	0.550
Positive Predictive Value	0.657
Nr of predictions	46

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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_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_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_01073	SAM links to Rfam database...	0.56	0.47	0.67	16	4347	9	1	7	1	18
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_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
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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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 Pknots - scored higher in this pairwise comparison

1. Total counts & total scores for Pknots

2. Individual counts for Pknots [ 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 ]