CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Cylofold		ContextFold
MCC	0.701	>	0.566
Average MCC ± 95% Confidence Intervals	0.777 ± 0.078	>	0.556 ± 0.084
Sensitivity	0.673	>	0.505
Positive Predictive Value	0.734	>	0.640
Total TP	669	>	502
Total TN	135259	<	135386
Total FP	262	<	294
Total FP CONTRA	34	>	26
Total FP INCONS	208	<	256
Total FP COMP	20	>	12
Total FN	325	<	492
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Cylofold and ContextFold. 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 Cylofold and ContextFold).
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 Cylofold and ContextFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and ContextFold. 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 Cylofold and ContextFold).

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Performance of Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

Total Base Pair Counts
Total TP	669
Total TN	135259
Total FP	262
Total FP CONTRA	34
Total FP INCONS	208
Total FP COMP	20
Total FN	325

Total Scores
MCC	0.701
Average MCC ± 95% Confidence Intervals	0.777 ± 0.078
Sensitivity	0.673
Positive Predictive Value	0.734
Nr of predictions	47

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00408	-	0.17	0.15	0.20	11	32329	45	3	42	0	60
ASE_00429	-	0.38	0.33	0.43	22	28152	33	0	29	4	44
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.78	0.79	0.79	11	932	3	0	3	0	3
PDB_00018	-	0.90	0.90	0.90	18	1015	2	2	0	0	2
PDB_00020	-	0.79	0.75	0.83	15	762	3	0	3	0	5
PDB_00041	-	1.00	1.00	1.00	12	618	0	0	0	0	0
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	-	0.94	0.94	0.94	34	4150	2	2	0	0	2
PDB_00124	-	0.86	0.90	0.82	9	485	2	2	0	0	1
PDB_00128	-	0.78	0.79	0.79	11	482	3	0	3	0	3
PDB_00134	-	0.94	1.00	0.89	8	369	1	1	0	0	0
PDB_00138	-	0.94	1.00	0.89	8	369	1	1	0	0	0
PDB_00209	-	0.96	1.00	0.92	11	549	1	1	0	0	0
PDB_00243	-	1.00	1.00	1.00	12	618	0	0	0	0	0
PDB_00352	-	0.90	0.95	0.86	18	1204	3	2	1	0	1
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00713	-	0.24	0.24	0.26	5	1997	14	0	14	0	16
PDB_00716	HDV_ribozyme links to Rfam database...	0.68	0.70	0.67	16	2677	9	0	8	1	7
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...	0.43	0.42	0.45	10	2256	12	0	12	0	14
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	-	1.00	1.00	1.00	15	1066	0	0	0	0	0
PDB_00874	-	0.21	0.20	0.25	4	930	12	0	12	0	16
PDB_00886	-	0.34	0.35	0.35	14	4146	26	0	26	0	26
PDB_00918	-	0.93	1.00	0.88	7	317	1	1	0	0	0
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	-	1.00	1.00	1.00	20	1108	0	0	0	0	0
PDB_01059	-	0.88	1.00	0.78	7	222	2	2	0	0	0
PDB_01073	SAM links to Rfam database...	0.75	0.65	0.88	22	4346	4	2	1	1	12
PDB_01194	-	0.97	0.93	1.00	14	482	0	0	0	0	1
PDB_01201	-	0.95	0.91	1.00	20	1108	0	0	0	0	2
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01260	-	0.41	0.36	0.47	9	1811	10	0	10	0	16
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.90	0.87	0.93	13	889	1	1	0	0	2
RFA_00632	HDV_ribozyme links to Rfam database...	0.54	0.54	0.56	15	4068	12	2	10	0	13
RFA_00636	HDV_ribozyme links to Rfam database...	0.78	0.82	0.74	23	3974	8	7	1	0	5
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	4	0	0	4	0
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...	0.97	1.00	0.95	18	1934	1	1	0	0	0
RFA_00770	Corona_pk3 links to Rfam database...	0.88	0.78	1.00	14	2002	3	0	0	3	4
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	4	1	0	3	0
RFA_00779	Corona_pk3 links to Rfam database...	0.97	0.94	1.00	17	1936	0	0	0	0	1
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

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Performance of ContextFold - scored lower in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	502
Total TN	135386
Total FP	294
Total FP CONTRA	26
Total FP INCONS	256
Total FP COMP	12
Total FN	492

Total Scores
MCC	0.566
Average MCC ± 95% Confidence Intervals	0.556 ± 0.084
Sensitivity	0.505
Positive Predictive Value	0.640
Nr of predictions	47

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00408	-	0.95	0.93	0.97	66	32317	6	2	0	4	5
ASE_00429	-	0.94	0.88	1.00	58	28145	3	0	0	3	8
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.42	0.36	0.50	5	936	5	0	5	0	9
PDB_00018	-	0.22	0.20	0.27	4	1020	11	2	9	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	-	0.70	0.50	1.00	5	491	0	0	0	0	5
PDB_00128	-	0.75	0.57	1.00	8	488	0	0	0	0	6
PDB_00134	-	0.57	0.50	0.67	4	372	2	0	2	0	4
PDB_00138	-	-0.02	0.00	0.00	0	372	6	1	5	0	8
PDB_00209	-	0.67	0.45	1.00	5	556	0	0	0	0	6
PDB_00243	-	0.50	0.42	0.63	5	622	3	0	3	0	7
PDB_00352	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00571	tRNA links to Rfam database...	0.85	0.76	0.95	19	3301	1	1	0	0	6
PDB_00713	-	0.42	0.38	0.47	8	1999	9	0	9	0	13
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2687	14	0	14	0	23
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.72	0.63	0.83	5	372	1	0	1	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	-	-0.02	0.00	0.00	0	929	17	0	17	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4151	35	0	35	0	40
PDB_00918	-	0.67	0.57	0.80	4	320	1	0	1	0	3
PDB_01009	tRNA links to Rfam database...	0.90	0.90	0.90	19	2464	3	0	2	1	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	0.33	6	1110	12	0	12	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01073	SAM links to Rfam database...	0.48	0.44	0.54	15	4343	13	2	11	0	19
PDB_01194	-	0.77	0.60	1.00	9	487	0	0	0	0	6
PDB_01201	-	0.53	0.41	0.69	9	1115	4	0	4	0	13
PDB_01203	-	0.77	0.68	0.87	13	1161	2	2	0	0	6
PDB_01260	-	0.52	0.36	0.75	9	1818	3	0	3	0	16
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.73	0.60	0.90	9	893	3	1	0	2	6
RFA_00632	HDV_ribozyme links to Rfam database...	0.25	0.25	0.26	7	4068	20	1	19	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.52	0.43	0.63	12	3986	7	0	7	0	16
RFA_00767	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	3	3	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1876	5	2	3	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	4	4	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	2001	5	2	3	0	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_00809	RydC links to Rfam database...	0.39	0.31	0.50	5	2135	6	0	5	1	11

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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 Cylofold - scored higher in this pairwise comparison

1. Total counts & total scores for Cylofold

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

Performance of ContextFold - scored lower in this pairwise comparison

1. Total counts & total scores for ContextFold

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