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		McQFold
MCC	0.764	>	0.699
Average MCC ± 95% Confidence Intervals	0.800 ± 0.075	>	0.752 ± 0.086
Sensitivity	0.742	>	0.673
Positive Predictive Value	0.791	>	0.732
Total TP	636	>	577
Total TN	74778	<	74794
Total FP	184	<	225
Total FP CONTRA	31	>	30
Total FP INCONS	137	<	181
Total FP COMP	16	>	14
Total FN	221	<	280
P-value	3.56938820447e-08

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Performance plots

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

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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	636
Total TN	74778
Total FP	184
Total FP CONTRA	31
Total FP INCONS	137
Total FP COMP	16
Total FN	221

Total Scores
MCC	0.764
Average MCC ± 95% Confidence Intervals	0.800 ± 0.075
Sensitivity	0.742
Positive Predictive Value	0.791
Nr of predictions	45

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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
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 McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	577
Total TN	74794
Total FP	225
Total FP CONTRA	30
Total FP INCONS	181
Total FP COMP	14
Total FN	280

Total Scores
MCC	0.699
Average MCC ± 95% Confidence Intervals	0.752 ± 0.086
Sensitivity	0.673
Positive Predictive Value	0.732
Nr of predictions	45

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2. Individual counts for McQFold [ 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	-	0.19	0.20	0.21	4	1016	15	2	13	0	16
PDB_00020	-	0.75	0.65	0.87	13	765	2	0	2	0	7
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	-	0.33	0.33	0.33	12	4150	24	0	24	0	24
PDB_00124	-	0.86	0.90	0.82	9	485	2	2	0	0	1
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	-	0.94	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	-	0.86	0.79	0.94	15	1209	1	0	1	0	4
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00713	-	0.43	0.43	0.45	9	1996	11	0	11	0	12
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...	0.86	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	-	0.49	0.44	0.56	18	4721	14	0	14	0	23
PDB_00857	-	1.00	1.00	1.00	15	1066	0	0	0	0	0
PDB_00874	-	-0.02	0.00	0.00	0	928	18	0	18	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4147	39	0	39	0	40
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	-	0.30	0.30	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.88	1.00	0.78	7	222	2	2	0	0	0
PDB_01073	SAM links to Rfam database...	0.52	0.47	0.57	16	4343	13	2	10	1	18
PDB_01194	-	0.89	0.87	0.93	13	482	1	1	0	0	2
PDB_01201	-	0.88	0.77	1.00	17	1111	0	0	0	0	5
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01260	-	0.92	0.92	0.92	23	1805	2	1	1	0	2
PDB_01281	-	-0.04	0.00	0.00	0	365	13	0	13	0	14
PDB_01299	-	0.71	0.67	0.77	10	890	3	1	2	0	5
RFA_00632	HDV_ribozyme links to Rfam database...	0.88	0.89	0.86	25	4066	4	3	1	0	3
RFA_00636	HDV_ribozyme links to Rfam database...	0.73	0.71	0.74	20	3978	7	5	2	0	8
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	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...	0.85	0.94	0.77	17	1931	5	4	1	0	1
RFA_00770	Corona_pk3 links to Rfam database...	0.88	0.78	1.00	14	2002	4	0	0	4	4
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	5	1	0	4	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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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 McQFold - scored lower in this pairwise comparison

1. Total counts & total scores for McQFold

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