CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Fold		RNAshapes
MCC	0.453	>	0.416
Average MCC ± 95% Confidence Intervals	0.528 ± 0.080	>	0.494 ± 0.080
Sensitivity	0.431	>	0.395
Positive Predictive Value	0.485	>	0.448
Total TP	508	>	465
Total TN	158458	<	158467
Total FP	557	<	588
Total FP CONTRA	71	<	84
Total FP INCONS	469	<	490
Total FP COMP	17	>	14
Total FN	670	<	713
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Fold and RNAshapes. 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 Fold and RNAshapes).
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 Fold and RNAshapes).
Comparison of average Matthews Correlation Coefficients (MCCs) for Fold and RNAshapes. 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 Fold and RNAshapes).

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Performance of Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

Total Base Pair Counts
Total TP	508
Total TN	158458
Total FP	557
Total FP CONTRA	71
Total FP INCONS	469
Total FP COMP	17
Total FN	670

Total Scores
MCC	0.453
Average MCC ± 95% Confidence Intervals	0.528 ± 0.080
Sensitivity	0.431
Positive Predictive Value	0.485
Nr of predictions	53

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2. Individual counts for Fold [ 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	-	0.59	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	-	0.39	0.37	0.44	7	1209	9	0	9	0	12
PDB_00370	-	0.09	0.12	0.07	3	15179	45	12	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...	0.85	0.76	0.95	19	3301	1	1	0	0	6
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	-	0.09	0.10	0.11	2	928	16	2	14	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...	0.46	0.52	0.41	11	2458	16	5	11	0	10
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	-	0.68	0.63	0.74	34	12674	12	0	12	0	20
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	0	6	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	-	0.10	0.10	0.12	4	12056	30	7	23	0	37
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	-	0.74	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...	0.39	0.39	0.39	11	4067	17	2	15	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...	0.44	0.44	0.44	8	1873	10	1	9	0	10
RFA_00768	Corona_pk3 links to Rfam database...	0.45	0.44	0.47	8	1874	10	1	8	1	10
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	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	3	1	0	2	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	2000	18	2	14	2	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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Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

Total Base Pair Counts
Total TP	465
Total TN	158467
Total FP	588
Total FP CONTRA	84
Total FP INCONS	490
Total FP COMP	14
Total FN	713

Total Scores
MCC	0.416
Average MCC ± 95% Confidence Intervals	0.494 ± 0.080
Sensitivity	0.395
Positive Predictive Value	0.448
Nr of predictions	53

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2. Individual counts for RNAshapes [ 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	0.06	3	15178	44	12	32	0	22
PDB_00447	-	0.44	0.39	0.52	17	7107	16	6	10	0	27
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_00804	-	0.19	0.20	0.18	10	15345	46	9	36	1	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	-	0.35	0.29	0.43	12	4725	16	0	16	0	29
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	-	0.42	0.37	0.49	20	12679	22	0	21	1	34
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...	0.54	0.50	0.58	26	10108	21	2	17	2	26
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	-	0.21	0.20	0.23	8	12055	28	5	22	1	33
PDB_01260	-	0.56	0.48	0.67	12	1812	6	0	6	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	-	0.18	0.23	0.15	9	9119	52	13	39	0	30
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...	0.42	0.43	0.43	12	3977	16	2	14	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...	0.36	0.38	0.35	6	2128	11	1	10	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 Fold - scored higher in this pairwise comparison

1. Total counts & total scores for Fold

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

Performance of RNAshapes - scored lower in this pairwise comparison

1. Total counts & total scores for RNAshapes

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