CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	IPknot		Contrafold
MCC	0.489	>	0.458
Average MCC ± 95% Confidence Intervals	0.564 ± 0.083	>	0.525 ± 0.083
Sensitivity	0.435	>	0.435
Positive Predictive Value	0.556	>	0.491
Total TP	513	>	512
Total TN	158584	>	158463
Total FP	421	<	548
Total FP CONTRA	53	<	63
Total FP INCONS	356	<	468
Total FP COMP	12	<	17
Total FN	665	<	666
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of IPknot and Contrafold. 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 IPknot and Contrafold).
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 IPknot and Contrafold).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and Contrafold. 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 IPknot and Contrafold).

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Performance of IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	513
Total TN	158584
Total FP	421
Total FP CONTRA	53
Total FP INCONS	356
Total FP COMP	12
Total FN	665

Total Scores
MCC	0.489
Average MCC ± 95% Confidence Intervals	0.564 ± 0.083
Sensitivity	0.435
Positive Predictive Value	0.556
Nr of predictions	53

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2. Individual counts for IPknot [ 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...	0.71	0.71	0.71	10	932	4	0	4	0	4
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	-	0.73	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	-	0.17	0.20	0.18	2	485	9	2	7	0	8
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	-	0.76	0.58	1.00	7	623	0	0	0	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	15225	0	0	0	0	25
PDB_00447	-	0.41	0.25	0.69	11	7124	5	0	5	0	33
PDB_00571	tRNA links to Rfam database...	0.79	0.76	0.83	19	3298	4	2	2	0	6
PDB_00713	-	0.52	0.43	0.64	9	2002	5	0	5	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	21	0	21	0	23
PDB_00804	-	0.23	0.24	0.23	12	15348	42	10	30	2	38
PDB_00828	Purine links to Rfam database...	0.90	0.81	1.00	22	2463	0	0	0	0	5
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	-	0.93	0.87	1.00	13	1068	0	0	0	0	2
PDB_00874	-	0.10	0.10	0.13	2	931	13	2	11	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...	0.71	0.81	0.63	17	2458	10	5	5	0	4
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	-	0.32	0.26	0.40	14	12685	21	0	21	0	40
PDB_01073	SAM links to Rfam database...	0.80	0.65	1.00	22	4349	1	0	0	1	12
PDB_01092	glmS links to Rfam database...	0.73	0.63	0.85	33	10114	8	1	5	2	19
PDB_01194	-	0.52	0.33	0.83	5	490	1	1	0	0	10
PDB_01201	-	0.61	0.45	0.83	10	1116	2	0	2	0	12
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01250	-	0.18	0.15	0.22	6	12063	21	5	16	0	35
PDB_01260	-	0.58	0.48	0.71	12	1813	5	1	4	0	13
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.71	0.67	0.77	10	890	3	2	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...	0.42	0.36	0.50	10	4075	11	0	10	1	18
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...	0.74	0.56	1.00	10	1881	0	0	0	0	8
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...	0.54	0.56	0.53	10	1934	9	4	5	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...	0.61	0.56	0.67	10	1938	8	1	4	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	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...	0.47	0.38	0.60	6	2135	4	0	4	0	10

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Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

Total Base Pair Counts
Total TP	512
Total TN	158463
Total FP	548
Total FP CONTRA	63
Total FP INCONS	468
Total FP COMP	17
Total FN	666

Total Scores
MCC	0.458
Average MCC ± 95% Confidence Intervals	0.525 ± 0.083
Sensitivity	0.435
Positive Predictive Value	0.491
Nr of predictions	53

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2. Individual counts for Contrafold [ 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	-	0.18	0.20	0.20	4	1015	16	2	14	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	-	0.25	0.25	0.29	4	616	10	0	10	0	12
PDB_00123	-	-0.01	0.00	0.00	0	4151	35	0	35	0	36
PDB_00124	-	-0.02	0.00	0.00	0	486	10	2	8	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	-	0.56	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	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00370	-	0.00	0.00	0.00	0	15185	40	4	36	0	25
PDB_00447	-	0.66	0.55	0.80	24	7110	6	6	0	0	20
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00713	-	0.58	0.57	0.60	12	1996	8	1	7	0	9
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	1	0	0	1	6
PDB_00829	Purine links to Rfam database...	0.84	0.75	0.95	18	2259	1	0	1	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	-	0.73	0.60	0.90	9	1071	1	0	1	0	6
PDB_00874	-	-0.02	0.00	0.00	0	928	19	0	18	1	20
PDB_00886	-	-0.01	0.00	0.00	0	4146	40	0	40	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...	0.81	0.74	0.89	17	2259	3	1	1	1	6
PDB_01040	-	0.29	0.30	0.30	6	1108	14	0	14	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.41	0.37	0.45	20	12676	24	0	24	0	34
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...	0.70	0.65	0.76	34	10108	14	2	9	3	18
PDB_01194	-	-0.03	0.00	0.00	0	485	11	0	11	0	15
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.70	0.68	0.72	13	1158	5	3	2	0	6
PDB_01250	-	0.17	0.15	0.21	6	12061	23	5	18	0	35
PDB_01260	-	0.64	0.56	0.74	14	1811	5	1	4	0	11
PDB_01281	-	-0.04	0.00	0.00	0	364	14	0	14	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	9117	64	9	54	1	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.38	0.39	0.37	11	4065	19	0	19	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.60	0.64	0.56	18	3973	14	4	10	0	10
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	2	0	0	2	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...	0.54	0.56	0.53	10	1934	9	4	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	5	0	2	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...	0.68	0.56	0.83	10	1941	2	0	2	0	8
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	0	8	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 IPknot - scored higher in this pairwise comparison

1. Total counts & total scores for IPknot

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

Performance of Contrafold - scored lower in this pairwise comparison

1. Total counts & total scores for Contrafold

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