CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	PPfold(seed)		RNASampler(seed)
MCC	0.862	>	0.713
Average MCC ± 95% Confidence Intervals	0.759 ± 0.089	>	0.561 ± 0.111
Sensitivity	0.777	>	0.571
Positive Predictive Value	0.957	>	0.890
Total TP	647	>	476
Total TN	374211	<	374352
Total FP	55	<	109
Total FP CONTRA	6	<	19
Total FP INCONS	23	<	40
Total FP COMP	26	<	50
Total FN	186	<	357
P-value	5.19332990918e-08

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Performance plots

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

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

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

Total Base Pair Counts
Total TP	647
Total TN	374211
Total FP	55
Total FP CONTRA	6
Total FP INCONS	23
Total FP COMP	26
Total FN	186

Total Scores
MCC	0.862
Average MCC ± 95% Confidence Intervals	0.759 ± 0.089
Sensitivity	0.777
Positive Predictive Value	0.957
Nr of predictions	27

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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
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_00626	rne5 links to Rfam database...	0.94	0.89	1.00	77	56539	1	0	0	1	10
RFA_00627	rne5 links to Rfam database...	0.95	0.91	1.00	79	56874	4	0	0	4	8
RFA_00628	rne5 links to Rfam database...	0.95	0.91	1.00	78	57213	2	0	0	2	8
RFA_00630	rne5 links to Rfam database...	0.91	0.85	0.97	74	56877	5	0	2	3	13
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
RFA_00814	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	25164	2	0	0	2	5
RFA_00816	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	23183	2	0	0	2	4
RFA_00817	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	21908	1	0	0	1	4
RFA_00818	R2_retro_el links to Rfam database...	0.94	0.88	1.00	36	20265	2	0	0	2	5
RFA_00819	R2_retro_el links to Rfam database...	0.95	0.90	1.00	37	27929	2	0	0	2	4

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

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

Total Base Pair Counts
Total TP	476
Total TN	374352
Total FP	109
Total FP CONTRA	19
Total FP INCONS	40
Total FP COMP	50
Total FN	357

Total Scores
MCC	0.713
Average MCC ± 95% Confidence Intervals	0.561 ± 0.111
Sensitivity	0.571
Positive Predictive Value	0.890
Nr of predictions	27

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00390	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00416	Hammerhead_3 links to Rfam database...	0.63	0.40	1.00	6	1479	1	0	0	1	9
RFA_00433	Hammerhead_3 links to Rfam database...	0.63	0.40	1.00	6	1425	1	0	0	1	9
RFA_00626	rne5 links to Rfam database...	0.80	0.64	1.00	56	56560	5	0	0	5	31
RFA_00627	rne5 links to Rfam database...	0.77	0.63	0.93	55	56894	8	0	4	4	32
RFA_00628	rne5 links to Rfam database...	0.78	0.64	0.95	55	57233	12	0	3	9	31
RFA_00630	rne5 links to Rfam database...	0.77	0.66	0.90	57	56890	15	0	6	9	30
RFA_00654	Vimentin3 links to Rfam database...	0.39	0.28	0.56	5	2406	4	1	3	0	13
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00749	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00764	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00765	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00767	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1878	3	3	0	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.52	0.39	0.70	7	2006	3	3	0	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.50	0.69	9	1940	4	4	0	0	9
RFA_00779	Corona_pk3 links to Rfam database...	0.65	0.56	0.77	10	1940	3	3	0	0	8
RFA_00808	RydC links to Rfam database...	0.58	0.56	0.60	9	2001	6	0	6	0	7
RFA_00809	RydC links to Rfam database...	0.36	0.38	0.35	6	2128	11	1	10	0	10
RFA_00814	R2_retro_el links to Rfam database...	0.87	0.78	0.97	32	25167	6	0	1	5	9
RFA_00816	R2_retro_el links to Rfam database...	0.86	0.76	0.97	31	23188	6	0	1	5	10
RFA_00817	R2_retro_el links to Rfam database...	0.86	0.76	0.97	31	21913	1	0	1	0	10
RFA_00818	R2_retro_el links to Rfam database...	0.86	0.73	1.00	30	20271	6	0	0	6	11
RFA_00819	R2_retro_el links to Rfam database...	0.88	0.78	1.00	32	27934	5	0	0	5	9

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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 PPfold(seed) - scored higher in this pairwise comparison

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

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

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

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

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