CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	HotKnots		RDfolder
MCC	0.534	>	0.508
Average MCC ± 95% Confidence Intervals	0.604 ± 0.106	>	0.545 ± 0.084
Sensitivity	0.510	>	0.432
Positive Predictive Value	0.569	<	0.609
Total TP	445	>	377
Total TN	76816	<	76979
Total FP	348	>	245
Total FP CONTRA	35	>	22
Total FP INCONS	302	>	220
Total FP COMP	11	>	3
Total FN	428	<	496
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of HotKnots and RDfolder. 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 HotKnots and RDfolder).
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 HotKnots and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for HotKnots and RDfolder. 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 HotKnots and RDfolder).

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Performance of HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

Total Base Pair Counts
Total TP	445
Total TN	76816
Total FP	348
Total FP CONTRA	35
Total FP INCONS	302
Total FP COMP	11
Total FN	428

Total Scores
MCC	0.534
Average MCC ± 95% Confidence Intervals	0.604 ± 0.106
Sensitivity	0.510
Positive Predictive Value	0.569
Nr of predictions	46

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2. Individual counts for HotKnots [ 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	-	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	4151	35	0	35	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	-	0.79	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	-	0.71	0.58	0.88	7	622	1	0	1	0	5
PDB_00352	-	0.89	0.79	1.00	15	1210	0	0	0	0	4
PDB_00571	tRNA links to Rfam database...	0.17	0.16	0.19	4	3300	17	6	11	0	21
PDB_00713	-	0.43	0.43	0.45	9	1996	11	0	11	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2678	24	1	22	1	23
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	-	1.00	1.00	1.00	15	1066	0	0	0	0	0
PDB_00874	-	0.10	0.10	0.14	2	932	12	2	10	0	18
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...	0.52	0.57	0.48	12	2460	13	5	8	0	9
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	0.33	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...	0.81	0.74	0.89	25	4343	4	2	1	1	9
PDB_01194	-	0.93	0.93	0.93	14	481	1	1	0	0	1
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.71	0.63	0.80	12	1161	3	2	1	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	-	0.74	0.67	0.83	10	891	2	1	1	0	5
RFA_00632	HDV_ribozyme links to Rfam database...	0.38	0.39	0.37	11	4065	19	2	17	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.42	0.43	0.43	12	3977	16	2	14	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1870	3	3	0	0	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1934	21	0	19	2	18
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1999	20	0	17	3	18
RFA_00773	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1934	22	0	19	3	18
RFA_00779	Corona_pk3 links to Rfam database...	0.87	0.94	0.81	17	1932	4	3	1	0	1
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 RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

Total Base Pair Counts
Total TP	377
Total TN	76979
Total FP	245
Total FP CONTRA	22
Total FP INCONS	220
Total FP COMP	3
Total FN	496

Total Scores
MCC	0.508
Average MCC ± 95% Confidence Intervals	0.545 ± 0.084
Sensitivity	0.432
Positive Predictive Value	0.609
Nr of predictions	46

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2. Individual counts for RDfolder [ 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	-	0.41	0.35	0.50	7	766	7	0	7	0	13
PDB_00041	-	0.70	0.50	1.00	6	624	0	0	0	0	6
PDB_00053	-	0.67	0.45	1.00	5	430	0	0	0	0	6
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	0.75	0.61	0.92	22	4162	2	2	0	0	14
PDB_00124	-	0.70	0.50	1.00	5	491	0	0	0	0	5
PDB_00128	-	0.84	0.71	1.00	10	486	0	0	0	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	-	0.48	0.37	0.64	7	1214	4	0	4	0	12
PDB_00571	tRNA links to Rfam database...	0.39	0.36	0.43	9	3300	12	0	12	0	16
PDB_00713	-	0.46	0.43	0.50	9	1998	9	0	9	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2684	18	1	16	1	23
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	-	0.11	0.10	0.15	4	4726	23	0	23	0	37
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	-	0.37	0.35	0.41	14	4152	20	0	20	0	26
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.37	0.33	0.41	7	2468	10	0	10	0	14
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_01073	SAM links to Rfam database...	0.43	0.38	0.50	13	4345	13	1	12	0	21
PDB_01194	-	0.52	0.33	0.83	5	490	1	1	0	0	10
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	-0.01	0.00	0.00	0	1166	10	0	10	0	19
PDB_01260	-	-0.01	0.00	0.00	0	1817	13	0	13	0	25
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	-0.01	0.00	0.00	0	897	6	2	4	0	15
RFA_00632	HDV_ribozyme links to Rfam database...	0.62	0.54	0.71	15	4074	6	1	5	0	13
RFA_00636	HDV_ribozyme links to Rfam database...	0.65	0.64	0.67	18	3978	9	3	6	0	10
RFA_00767	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1882	0	0	0	0	9
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...	0.50	0.50	0.50	9	1935	9	4	5	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.47	0.39	0.58	7	2004	5	1	4	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.67	0.50	0.90	9	1943	1	1	0	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	3	0	2	1	7
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 HotKnots - scored higher in this pairwise comparison

1. Total counts & total scores for HotKnots

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

Performance of RDfolder - scored lower in this pairwise comparison

1. Total counts & total scores for RDfolder

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