CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MaxExpect		RNAwolf
MCC	0.440	>	0.362
Average MCC ± 95% Confidence Intervals	0.520 ± 0.080	>	0.397 ± 0.078
Sensitivity	0.414	>	0.353
Positive Predictive Value	0.476	>	0.380
Total TP	488	>	416
Total TN	158481	>	158411
Total FP	547	<	724
Total FP CONTRA	64	<	111
Total FP INCONS	473	<	568
Total FP COMP	10	<	45
Total FN	690	<	762
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MaxExpect and RNAwolf. 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 MaxExpect and RNAwolf).
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 MaxExpect and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for MaxExpect and RNAwolf. 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 MaxExpect and RNAwolf).

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Performance of MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

Total Base Pair Counts
Total TP	488
Total TN	158481
Total FP	547
Total FP CONTRA	64
Total FP INCONS	473
Total FP COMP	10
Total FN	690

Total Scores
MCC	0.440
Average MCC ± 95% Confidence Intervals	0.520 ± 0.080
Sensitivity	0.414
Positive Predictive Value	0.476
Nr of predictions	53

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2. Individual counts for MaxExpect [ 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	-	-0.02	0.00	0.00	0	488	8	2	6	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	-	0.83	0.74	0.93	14	1210	1	0	1	0	5
PDB_00370	-	0.09	0.12	0.07	3	15182	40	10	30	0	22
PDB_00447	-	0.27	0.25	0.31	11	7104	25	6	19	0	33
PDB_00571	tRNA links to Rfam database...	0.42	0.36	0.50	9	3303	9	2	7	0	16
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_00804	-	0.31	0.32	0.31	16	15348	38	6	30	2	34
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	-	0.67	0.60	0.75	9	1069	3	0	3	0	6
PDB_00874	-	0.10	0.10	0.13	2	930	14	2	12	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...	0.51	0.57	0.46	12	2459	14	5	9	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	-	0.35	0.30	0.41	16	12681	23	0	23	0	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...	0.75	0.63	0.89	33	10116	6	0	4	2	19
PDB_01194	-	0.77	0.60	1.00	9	487	0	0	0	0	6
PDB_01201	-	0.82	0.68	1.00	15	1113	0	0	0	0	7
PDB_01203	-	0.71	0.63	0.80	12	1161	3	2	1	0	7
PDB_01250	-	0.13	0.12	0.15	5	12057	28	3	25	0	36
PDB_01260	-	0.64	0.48	0.86	12	1816	2	0	2	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...	0.34	0.36	0.33	10	4065	20	2	18	0	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.41	0.43	0.40	12	3975	18	2	16	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...	0.47	0.44	0.50	8	1875	8	1	7	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...	0.63	0.56	0.71	10	2002	7	0	4	3	8
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...	0.61	0.56	0.67	10	1938	5	2	3	0	8
RFA_00808	RydC links to Rfam database...	0.62	0.56	0.69	9	2003	4	0	4	0	7
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	0	10

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Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	416
Total TN	158411
Total FP	724
Total FP CONTRA	111
Total FP INCONS	568
Total FP COMP	45
Total FN	762

Total Scores
MCC	0.362
Average MCC ± 95% Confidence Intervals	0.397 ± 0.078
Sensitivity	0.353
Positive Predictive Value	0.380
Nr of predictions	53

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2. Individual counts for RNAwolf [ 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...	0.42	0.36	0.50	5	936	6	0	5	1	9
PDB_00018	-	0.18	0.15	0.25	3	1023	9	2	7	0	17
PDB_00020	-	0.39	0.35	0.47	7	765	8	0	8	0	13
PDB_00041	-	0.61	0.50	0.75	6	622	2	0	2	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	0	5
PDB_00056	-	-0.02	0.00	0.00	0	615	15	0	15	0	16
PDB_00123	-	0.31	0.33	0.30	12	4146	28	4	24	0	24
PDB_00124	-	-0.02	0.00	0.00	0	485	11	2	9	0	10
PDB_00128	-	0.84	0.71	1.00	10	486	0	0	0	0	4
PDB_00134	-	0.72	0.63	0.83	5	372	3	0	1	2	3
PDB_00138	-	-0.02	0.00	0.00	0	371	7	0	7	0	8
PDB_00209	-	0.74	0.55	1.00	6	555	0	0	0	0	5
PDB_00243	-	0.54	0.42	0.71	5	623	2	0	2	0	7
PDB_00352	-	0.67	0.58	0.79	11	1211	3	0	3	0	8
PDB_00370	-	0.34	0.48	0.25	12	15177	42	23	13	6	13
PDB_00447	-	0.22	0.20	0.25	9	7104	27	2	25	0	35
PDB_00571	tRNA links to Rfam database...	0.89	0.84	0.95	21	3299	2	1	0	1	4
PDB_00713	-	0.28	0.24	0.33	5	2001	11	0	10	1	16
PDB_00716	HDV_ribozyme links to Rfam database...	0.68	0.57	0.81	13	2685	3	0	3	0	10
PDB_00804	-	0.23	0.24	0.22	12	15345	53	6	37	10	38
PDB_00828	Purine links to Rfam database...	0.85	0.81	0.88	22	2460	3	1	2	0	5
PDB_00829	Purine links to Rfam database...	0.78	0.75	0.82	18	2256	4	1	3	0	6
PDB_00842	-	0.72	0.63	0.83	5	372	1	0	1	0	3
PDB_00851	-	0.34	0.34	0.35	14	4713	26	0	26	0	27
PDB_00857	-	0.57	0.60	0.56	9	1065	7	0	7	0	6
PDB_00874	-	-0.02	0.00	0.00	0	928	18	0	18	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4143	43	4	39	0	40
PDB_00918	-	-0.02	0.00	0.00	0	317	8	0	8	0	7
PDB_01009	tRNA links to Rfam database...	0.45	0.52	0.39	11	2457	18	6	11	1	10
PDB_01020	Purine links to Rfam database...	0.84	0.83	0.86	19	2256	5	1	2	2	4
PDB_01040	-	0.24	0.25	0.25	5	1108	15	1	14	0	15
PDB_01059	-	-0.03	0.00	0.00	0	226	5	1	4	0	7
PDB_01070	-	0.00	0.00	0.00	0	12665	55	8	47	0	54
PDB_01073	SAM links to Rfam database...	0.17	0.18	0.17	6	4336	29	3	26	0	28
PDB_01092	glmS links to Rfam database...	0.43	0.38	0.49	20	10112	23	2	19	2	32
PDB_01194	-	0.61	0.53	0.73	8	485	3	0	3	0	7
PDB_01201	-	0.75	0.68	0.83	15	1110	3	0	3	0	7
PDB_01203	-	-0.01	0.00	0.00	0	1165	11	0	11	0	19
PDB_01250	-	0.45	0.44	0.46	18	12051	21	11	10	0	23
PDB_01260	-	-0.01	0.00	0.00	0	1809	21	0	21	0	25
PDB_01281	-	-0.04	0.00	0.00	0	365	13	0	13	0	14
PDB_01299	-	0.65	0.53	0.80	8	893	2	0	2	0	7
PDB_01309	-	0.26	0.31	0.22	12	9126	42	14	28	0	27
RFA_00632	HDV_ribozyme links to Rfam database...	0.25	0.25	0.27	7	4069	22	1	18	3	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.40	0.39	0.41	11	3978	19	1	15	3	17
RFA_00767	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	8	1	6	1	10
RFA_00768	Corona_pk3 links to Rfam database...	0.50	0.44	0.57	8	1877	8	1	5	2	10
RFA_00769	Corona_pk3 links to Rfam database...	0.41	0.44	0.38	8	1932	13	3	10	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.51	0.50	0.53	9	1999	12	2	6	4	9
RFA_00773	Corona_pk3 links to Rfam database...	0.42	0.39	0.47	7	1938	12	1	7	4	11
RFA_00779	Corona_pk3 links to Rfam database...	0.26	0.28	0.26	5	1934	14	6	8	0	13
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	2	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	6	0	4	2	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 MaxExpect - scored higher in this pairwise comparison

1. Total counts & total scores for MaxExpect

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

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

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