CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		UNAFold
MCC	0.459	>	0.412
Average MCC ± 95% Confidence Intervals	0.535 ± 0.084	>	0.492 ± 0.082
Sensitivity	0.440	>	0.390
Positive Predictive Value	0.487	>	0.443
Total TP	518	>	460
Total TN	158442	<	158467
Total FP	562	<	591
Total FP CONTRA	69	<	86
Total FP INCONS	477	<	493
Total FP COMP	16	>	12
Total FN	660	<	718
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ProbKnot and UNAFold. 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 ProbKnot and UNAFold).
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 ProbKnot and UNAFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and UNAFold. 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 ProbKnot and UNAFold).

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	518
Total TN	158442
Total FP	562
Total FP CONTRA	69
Total FP INCONS	477
Total FP COMP	16
Total FN	660

Total Scores
MCC	0.459
Average MCC ± 95% Confidence Intervals	0.535 ± 0.084
Sensitivity	0.440
Positive Predictive Value	0.487
Nr of predictions	53

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2. Individual counts for ProbKnot [ 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	0	3	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	-	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	-	-0.02	0.00	0.00	0	488	8	2	6	0	10
PDB_00128	-	0.77	0.71	0.83	10	484	2	0	2	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.72	0.63	0.83	5	372	1	0	1	0	3
PDB_00209	-	0.56	0.45	0.71	5	554	2	0	2	0	6
PDB_00243	-	0.63	0.58	0.70	7	620	3	0	3	0	5
PDB_00352	-	0.86	0.79	0.94	15	1209	1	0	1	0	4
PDB_00370	-	0.09	0.12	0.07	3	15183	41	8	31	2	22
PDB_00447	-	0.27	0.25	0.30	11	7103	26	6	20	0	33
PDB_00571	tRNA links to Rfam database...	0.60	0.60	0.60	15	3296	10	6	4	0	10
PDB_00713	-	0.43	0.43	0.45	9	1996	12	0	11	1	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	22	0	21	1	23
PDB_00804	-	0.28	0.28	0.28	14	15350	38	6	30	2	36
PDB_00828	Purine links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	1.00	1.00	1.00	8	370	0	0	0	0	0
PDB_00851	-	0.45	0.39	0.53	16	4723	14	0	14	0	25
PDB_00857	-	0.80	0.80	0.80	12	1066	3	0	3	0	3
PDB_00874	-	0.05	0.05	0.08	1	933	12	2	10	0	19
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.67	0.57	0.80	4	320	1	0	1	0	3
PDB_01009	tRNA links to Rfam database...	0.54	0.57	0.52	12	2462	12	5	6	1	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	0.32	6	1109	13	0	13	0	14
PDB_01059	-	1.00	1.00	1.00	7	224	0	0	0	0	0
PDB_01070	-	0.33	0.30	0.38	16	12678	27	2	24	1	38
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...	0.73	0.63	0.85	33	10114	8	1	5	2	19
PDB_01194	-	0.69	0.60	0.82	9	485	2	0	2	0	6
PDB_01201	-	0.98	0.95	1.00	21	1107	0	0	0	0	1
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01250	-	0.22	0.20	0.25	8	12058	24	4	20	0	33
PDB_01260	-	0.53	0.48	0.60	12	1810	8	1	7	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...	0.40	0.39	0.41	11	4068	16	0	16	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.44	0.46	0.43	13	3975	17	0	17	0	15
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.44	0.44	0.44	8	1873	11	1	9	1	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...	0.59	0.56	0.63	10	2000	9	0	6	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00808	RydC links to Rfam database...	0.65	0.56	0.75	9	2004	3	0	3	0	7
RFA_00809	RydC links to Rfam database...	0.35	0.38	0.33	6	2127	12	1	11	0	10

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Performance of UNAFold - scored lower in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	460
Total TN	158467
Total FP	591
Total FP CONTRA	86
Total FP INCONS	493
Total FP COMP	12
Total FN	718

Total Scores
MCC	0.412
Average MCC ± 95% Confidence Intervals	0.492 ± 0.082
Sensitivity	0.390
Positive Predictive Value	0.443
Nr of predictions	53

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2. Individual counts for UNAFold [ 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	-	0.59	0.50	0.71	5	489	2	0	2	0	5
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	-	0.56	0.45	0.71	5	554	2	0	2	0	6
PDB_00243	-	0.63	0.58	0.70	7	620	3	0	3	0	5
PDB_00352	-	0.89	0.79	1.00	15	1210	0	0	0	0	4
PDB_00370	-	0.09	0.12	0.07	3	15179	45	12	31	2	22
PDB_00447	-	0.44	0.39	0.52	17	7107	16	6	10	0	27
PDB_00571	tRNA links to Rfam database...	0.21	0.20	0.24	5	3300	16	6	10	0	20
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	2677	24	5	19	0	23
PDB_00804	-	0.19	0.20	0.18	10	15344	46	10	36	0	40
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	-	0.45	0.39	0.53	16	4723	14	0	14	0	25
PDB_00857	-	0.54	0.40	0.75	6	1073	2	0	2	0	9
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	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.31	0.30	0.33	16	12671	34	2	31	1	38
PDB_01073	SAM links to Rfam database...	0.52	0.47	0.57	16	4343	13	2	10	1	18
PDB_01092	glmS links to Rfam database...	0.74	0.65	0.83	34	10112	8	1	6	1	18
PDB_01194	-	-0.02	0.00	0.00	0	488	8	0	8	0	15
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_01250	-	0.10	0.10	0.12	4	12056	30	7	23	0	37
PDB_01260	-	0.53	0.44	0.65	11	1813	6	0	6	0	14
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	9122	58	7	51	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.34	0.36	0.33	10	4065	20	2	18	0	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.43	0.43	0.44	12	3978	15	2	13	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	7	1	6	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...	0.61	0.56	0.67	10	2001	8	0	5	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	15	2	13	0	16
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

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

Performance of UNAFold - scored lower in this pairwise comparison

1. Total counts & total scores for UNAFold

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