CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PETfold_pre2.0(seed)		PPfold(seed)
MCC	0.765	>	0.386
Average MCC ± 95% Confidence Intervals	0.765 ± 0.068	>	0.308 ± 0.120
Sensitivity	0.665	>	0.176
Positive Predictive Value	0.883	>	0.852
Total TP	589	>	156
Total TN	121026	<	121510
Total FP	133	>	34
Total FP CONTRA	27	>	6
Total FP INCONS	51	>	21
Total FP COMP	55	>	7
Total FN	297	<	730
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of PETfold_pre2.0(seed) and PPfold(seed). 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 PETfold_pre2.0(seed) and PPfold(seed)).
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 PETfold_pre2.0(seed) and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and PPfold(seed). 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 PETfold_pre2.0(seed) and PPfold(seed)).

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Performance of PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

Total Base Pair Counts
Total TP	589
Total TN	121026
Total FP	133
Total FP CONTRA	27
Total FP INCONS	51
Total FP COMP	55
Total FN	297

Total Scores
MCC	0.765
Average MCC ± 95% Confidence Intervals	0.765 ± 0.068
Sensitivity	0.665
Positive Predictive Value	0.883
Nr of predictions	39

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2. Individual counts for PETfold_pre2.0(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_01001	tRNA links to Rfam database...	0.97	0.94	1.00	17	2128	1	0	0	1	1
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	3	0	0	3	0
RFA_00654	Vimentin3 links to Rfam database...	0.34	0.28	0.42	5	2403	7	0	7	0	13
RFA_00658	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1122	3	0	2	1	10
RFA_00664	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	984	3	0	2	1	10
RFA_00708	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1029	3	0	2	1	10
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	3	1	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	3	1	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	2002	4	3	1	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	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...	0.71	0.56	0.90	9	2006	1	1	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	4	0	4	0	10
SPR_00020	tRNA links to Rfam database...	1.00	1.00	1.00	20	2681	2	0	0	2	0
SPR_00137	tRNA links to Rfam database...	0.95	0.90	1.00	19	2907	3	0	0	3	2
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	1	0	0	1	0
SPR_00394	tRNA links to Rfam database...	0.98	0.95	1.00	20	3635	2	0	0	2	1
SPR_00402	tRNA links to Rfam database...	0.98	0.95	1.00	20	2536	2	0	0	2	1
SPR_00721	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	1	0	0	1	0
SPR_00816	tRNA links to Rfam database...	1.00	1.00	1.00	20	3466	2	0	0	2	0
SPR_01157	tRNA links to Rfam database...	1.00	1.00	1.00	21	2754	1	0	0	1	0
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.74	0.64	0.88	21	5541	4	1	2	1	12
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.73	0.62	0.88	21	5754	4	1	2	1	13
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.73	0.62	0.88	21	5436	4	1	2	1	13
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.75	0.59	0.95	20	5544	5	0	1	4	14
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.65	0.49	0.87	20	6305	5	1	2	2	21
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.73	0.62	0.88	21	5436	4	1	2	1	13
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.66	0.50	0.87	20	6763	5	1	2	2	20
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.71	0.55	0.91	21	6880	4	1	1	2	17
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.77	0.63	0.95	19	3721	4	0	1	3	11
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.76	0.61	0.96	22	5437	3	0	1	2	14
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.42	0.35	0.50	11	4731	14	0	11	3	20
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.71	0.56	0.91	20	5334	5	1	1	3	16

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Performance of PPfold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for PPfold(seed)

Total Base Pair Counts
Total TP	156
Total TN	121510
Total FP	34
Total FP CONTRA	6
Total FP INCONS	21
Total FP COMP	7
Total FN	730

Total Scores
MCC	0.386
Average MCC ± 95% Confidence Intervals	0.308 ± 0.120
Sensitivity	0.176
Positive Predictive Value	0.852
Nr of predictions	39

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2. Individual counts for PPfold(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_01001	tRNA links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	18
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	1	0	0	1	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	1	0	0	1	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00654	Vimentin3 links to Rfam database...	0.23	0.17	0.33	3	2406	6	0	6	0	15
RFA_00658	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	1126	1	0	0	1	12
RFA_00664	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	988	1	0	0	1	12
RFA_00708	Hammerhead_1 links to Rfam database...	0.38	0.14	1.00	2	1033	1	0	0	1	12
RFA_00749	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00764	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00765	s2m links to Rfam database...	0.78	0.75	0.82	9	892	2	0	2	0	3
RFA_00767	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1879	2	1	1	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	1	1	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	1	1	0	8
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.50	0.38	0.67	6	2136	3	0	3	0	10
SPR_00020	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	20
SPR_00137	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00277	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00394	tRNA links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	21
SPR_00402	tRNA links to Rfam database...	0.00	0.00	0.00	0	2556	0	0	0	0	21
SPR_00721	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00816	tRNA links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	20
SPR_01157	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	21
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	33
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5778	0	0	0	0	34
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	34
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	41
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6786	0	0	0	0	40
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	38
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3741	0	0	0	0	30
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	31
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5356	0	0	0	0	36

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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 PETfold_pre2.0(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for PETfold_pre2.0(seed)

2. Individual counts for PETfold_pre2.0(seed) [ download as .csv ]

Performance of PPfold(seed) - scored lower in this pairwise comparison

1. Total counts & total scores for PPfold(seed)

2. Individual counts for PPfold(seed) [ download as .csv ]