CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ProbKnot		MaxExpect
MCC	0.459	>	0.440
Average MCC ± 95% Confidence Intervals	0.535 ± 0.084	>	0.520 ± 0.080
Sensitivity	0.440	>	0.414
Positive Predictive Value	0.487	>	0.476
Total TP	518	>	488
Total TN	158442	<	158481
Total FP	562	>	547
Total FP CONTRA	69	>	64
Total FP INCONS	477	>	473
Total FP COMP	16	>	10
Total FN	660	<	690
P-value	3.56938820447e-08

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Performance plots

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

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Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	518
Total TN	158442
Total FP	562
Total FP CONTRA	69
Total FP INCONS	477
Total FP COMP	16
Total FN	660

Total Scores
MCC	0.459
Average MCC ± 95% Confidence Intervals	0.535 ± 0.084
Sensitivity	0.440
Positive Predictive Value	0.487
Nr of predictions	53

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2. Individual counts for ProbKnot [ 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	-	0.20	0.20	0.22	4	1017	14	2	12	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	-	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	-	-0.01	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	-	0.77	0.71	0.83	10	484	2	0	2	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.72	0.63	0.83	5	372	1	0	1	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	-	0.86	0.79	0.94	15	1209	1	0	1	0	4
PDB_00370	-	0.09	0.12	0.07	3	15183	41	8	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...	0.60	0.60	0.60	15	3296	10	6	4	0	10
PDB_00713	-	0.43	0.43	0.45	9	1996	12	0	11	1	12
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	22	0	21	1	23
PDB_00804	-	0.28	0.28	0.28	14	15350	38	6	30	2	36
PDB_00828	Purine links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
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	-	0.80	0.80	0.80	12	1066	3	0	3	0	3
PDB_00874	-	0.05	0.05	0.08	1	933	12	2	10	0	19
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.67	0.57	0.80	4	320	1	0	1	0	3
PDB_01009	tRNA links to Rfam database...	0.54	0.57	0.52	12	2462	12	5	6	1	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	-	1.00	1.00	1.00	7	224	0	0	0	0	0
PDB_01070	-	0.33	0.30	0.38	16	12678	27	2	24	1	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...	0.73	0.63	0.85	33	10114	8	1	5	2	19
PDB_01194	-	0.69	0.60	0.82	9	485	2	0	2	0	6
PDB_01201	-	0.98	0.95	1.00	21	1107	0	0	0	0	1
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01250	-	0.22	0.20	0.25	8	12058	24	4	20	0	33
PDB_01260	-	0.53	0.48	0.60	12	1810	8	1	7	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...	0.40	0.39	0.41	11	4068	16	0	16	0	17
RFA_00636	HDV_ribozyme links to Rfam database...	0.44	0.46	0.43	13	3975	17	0	17	0	15
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...	0.44	0.44	0.44	8	1873	11	1	9	1	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...	0.59	0.56	0.63	10	2000	9	0	6	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00808	RydC links to Rfam database...	0.65	0.56	0.75	9	2004	3	0	3	0	7
RFA_00809	RydC links to Rfam database...	0.35	0.38	0.33	6	2127	12	1	11	0	10

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Performance of MaxExpect - scored lower 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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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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

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

Performance of MaxExpect - scored lower in this pairwise comparison

1. Total counts & total scores for MaxExpect

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