CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Alterna		PPfold(seed)
MCC	0.543	>	0.501
Average MCC ± 95% Confidence Intervals	0.546 ± 0.113	>	0.414 ± 0.142
Sensitivity	0.529	>	0.297
Positive Predictive Value	0.565	<	0.852
Total TP	278	>	156
Total TN	62540	<	62849
Total FP	262	>	34
Total FP CONTRA	36	>	6
Total FP INCONS	178	>	21
Total FP COMP	48	>	7
Total FN	248	<	370
P-value	5.54865340847e-08

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Performance plots

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

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Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	278
Total TN	62540
Total FP	262
Total FP CONTRA	36
Total FP INCONS	178
Total FP COMP	48
Total FN	248

Total Scores
MCC	0.543
Average MCC ± 95% Confidence Intervals	0.546 ± 0.113
Sensitivity	0.529
Positive Predictive Value	0.565
Nr of predictions	29

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2. Individual counts for Alterna [ 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...	0.52	0.56	0.50	10	2125	10	3	7	0	8
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.93	0.93	14	1470	4	0	1	3	1
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...	-0.01	0.00	0.00	0	2399	16	2	14	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1116	5	0	3	2	5
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	10	0	10	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1025	4	0	3	1	7
RFA_00749	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00764	s2m links to Rfam database...	0.43	0.42	0.45	5	892	7	1	5	1	7
RFA_00765	s2m links to Rfam database...	0.81	0.67	1.00	8	895	2	0	0	2	4
RFA_00767	Corona_pk3 links to Rfam database...	0.54	0.50	0.60	9	1876	6	2	4	0	9
RFA_00768	Corona_pk3 links to Rfam database...	0.50	0.44	0.57	8	1877	9	0	6	3	10
RFA_00769	Corona_pk3 links to Rfam database...	0.38	0.39	0.39	7	1935	11	2	9	0	11
RFA_00770	Corona_pk3 links to Rfam database...	0.45	0.39	0.54	7	2003	9	0	6	3	11
RFA_00773	Corona_pk3 links to Rfam database...	0.45	0.39	0.54	7	1940	9	0	6	3	11
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...	-0.01	0.00	0.00	0	1999	19	3	14	2	16
RFA_00809	RydC links to Rfam database...	0.38	0.38	0.40	6	2130	11	0	9	2	10
SPR_00020	tRNA links to Rfam database...	0.79	0.75	0.83	15	2683	6	0	3	3	5
SPR_00137	tRNA links to Rfam database...	0.84	0.86	0.82	18	2904	10	0	4	6	3
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00394	tRNA links to Rfam database...	0.57	0.57	0.57	12	3634	14	5	4	5	9
SPR_00402	tRNA links to Rfam database...	0.62	0.62	0.62	13	2535	8	1	7	0	8
SPR_00721	tRNA links to Rfam database...	0.52	0.57	0.48	12	2901	15	1	12	2	9
SPR_00816	tRNA links to Rfam database...	0.32	0.35	0.29	7	3462	20	5	12	3	13
SPR_01157	tRNA links to Rfam database...	0.73	0.76	0.70	16	2752	8	0	7	1	5
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.77	0.73	0.81	22	3714	6	0	5	1	8
SRP_00341	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	4726	27	5	22	0	31

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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	62849
Total FP	34
Total FP CONTRA	6
Total FP INCONS	21
Total FP COMP	7
Total FN	370

Total Scores
MCC	0.501
Average MCC ± 95% Confidence Intervals	0.414 ± 0.142
Sensitivity	0.297
Positive Predictive Value	0.852
Nr of predictions	29

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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_00285	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3741	0	0	0	0	30
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	31

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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 Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

2. Individual counts for Alterna [ 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 ]