CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Contrafold		RNASLOpt
MCC	0.458	>	0.458
Average MCC ± 95% Confidence Intervals	0.525 ± 0.083	<	0.556 ± 0.082
Sensitivity	0.435	>	0.419
Positive Predictive Value	0.491	<	0.508
Total TP	512	>	493
Total TN	158463	<	158536
Total FP	548	>	487
Total FP CONTRA	63	>	58
Total FP INCONS	468	>	419
Total FP COMP	17	>	10
Total FN	666	<	685
P-value	0.187755798617

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Performance plots

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

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Performance of Contrafold - scored higher 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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Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

Total Base Pair Counts
Total TP	493
Total TN	158536
Total FP	487
Total FP CONTRA	58
Total FP INCONS	419
Total FP COMP	10
Total FN	685

Total Scores
MCC	0.458
Average MCC ± 95% Confidence Intervals	0.556 ± 0.082
Sensitivity	0.419
Positive Predictive Value	0.508
Nr of predictions	53

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2. Individual counts for RNASLOpt [ 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	-	0.75	0.65	0.87	13	765	2	0	2	0	7
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	-	0.70	0.50	1.00	5	491	0	0	0	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	-	0.67	0.45	1.00	5	556	0	0	0	0	6
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	15188	37	15	22	0	25
PDB_00447	-	0.30	0.25	0.37	11	7110	19	4	15	0	33
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...	-0.01	0.00	0.00	0	2680	22	0	21	1	23
PDB_00804	-	0.00	0.00	0.00	0	15350	52	6	44	2	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	-	0.45	0.39	0.53	16	4723	14	0	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	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...	0.90	0.90	0.90	19	2464	5	0	2	3	2
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	-	0.33	0.30	0.36	16	12676	28	2	26	0	38
PDB_01073	SAM links to Rfam database...	0.56	0.47	0.67	16	4347	9	0	8	1	18
PDB_01092	glmS links to Rfam database...	0.74	0.63	0.87	33	10115	7	1	4	2	19
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	-	0.74	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	-	0.49	0.36	0.69	9	1817	4	0	4	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
PDB_01309	-	-0.01	0.00	0.00	0	9118	62	9	53	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.59	0.57	0.62	16	4069	10	2	8	0	12
RFA_00636	HDV_ribozyme links to Rfam database...	0.65	0.64	0.67	18	3978	9	2	7	0	10
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...	0.61	0.56	0.67	10	1876	5	0	5	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
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...	0.59	0.56	0.63	10	1937	6	1	5	0	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...	0.40	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 Contrafold - scored higher in this pairwise comparison

1. Total counts & total scores for Contrafold

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

Performance of RNASLOpt - scored lower in this pairwise comparison

1. Total counts & total scores for RNASLOpt

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