CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	Multilign(seed)		RNAwolf
MCC	0.681	>	0.354
Average MCC ± 95% Confidence Intervals	0.547 ± 0.131	>	0.352 ± 0.108
Sensitivity	0.649	>	0.368
Positive Predictive Value	0.717	>	0.342
Total TP	576	>	327
Total TN	406244	>	406092
Total FP	315	<	786
Total FP CONTRA	48	<	142
Total FP INCONS	179	<	486
Total FP COMP	88	<	158
Total FN	312	<	561
P-value	5.19332990918e-08

^top

Performance plots

Comparison of performance of Multilign(seed) and RNAwolf. 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 Multilign(seed) and RNAwolf).
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 Multilign(seed) and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(seed) and RNAwolf. 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 Multilign(seed) and RNAwolf).

^top

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

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

Total Base Pair Counts
Total TP	576
Total TN	406244
Total FP	315
Total FP CONTRA	48
Total FP INCONS	179
Total FP COMP	88
Total FN	312

Total Scores
MCC	0.681
Average MCC ± 95% Confidence Intervals	0.547 ± 0.131
Sensitivity	0.649
Positive Predictive Value	0.717
Nr of predictions	23

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00416	Hammerhead_3 links to Rfam database...	0.57	0.53	0.62	8	1472	6	1	4	1	7
RFA_00619	-	0.37	0.41	0.34	16	22744	36	12	19	5	23
RFA_00626	rne5 links to Rfam database...	0.90	0.85	0.95	74	56538	20	0	4	16	13
RFA_00628	rne5 links to Rfam database...	0.92	0.88	0.95	76	57211	18	0	4	14	10
RFA_00630	rne5 links to Rfam database...	0.83	0.80	0.86	70	56872	29	0	11	18	17
RFA_00654	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2414	1	0	1	0	18
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_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...	0.61	0.56	0.67	10	1876	5	0	5	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	2	0	2	0	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	0	5	0	8
RFA_00808	RydC links to Rfam database...	0.60	0.56	0.64	9	2002	5	0	5	0	7
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	0	10
RFA_00816	R2_retro_el links to Rfam database...	1.00	1.00	1.00	41	23179	12	0	0	12	0
RFA_00817	R2_retro_el links to Rfam database...	0.77	0.78	0.76	32	21903	13	5	5	3	9
RFA_00818	R2_retro_el links to Rfam database...	0.85	0.80	0.89	33	20264	12	1	3	8	8
SRP_00241	Plant_SRP links to Rfam database...	0.48	0.50	0.46	41	45967	50	15	33	2	41
SRP_00331	Metazoa_SRP links to Rfam database...	0.69	0.69	0.70	60	37589	29	2	24	3	27
SRP_00340	Metazoa_SRP links to Rfam database...	0.59	0.61	0.57	50	41240	44	7	31	6	32

^top

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

Total Base Pair Counts
Total TP	327
Total TN	406092
Total FP	786
Total FP CONTRA	142
Total FP INCONS	486
Total FP COMP	158
Total FN	561

Total Scores
MCC	0.354
Average MCC ± 95% Confidence Intervals	0.352 ± 0.108
Sensitivity	0.368
Positive Predictive Value	0.342
Nr of predictions	23

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00416	Hammerhead_3 links to Rfam database...	0.80	0.80	0.80	12	1470	8	0	3	5	3
RFA_00619	-	0.15	0.18	0.13	7	22738	60	14	32	14	32
RFA_00626	rne5 links to Rfam database...	0.08	0.09	0.08	8	56511	99	24	73	2	79
RFA_00628	rne5 links to Rfam database...	0.58	0.57	0.59	49	57208	64	7	27	30	37
RFA_00630	rne5 links to Rfam database...	0.48	0.47	0.49	41	56869	66	9	34	23	46
RFA_00654	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2394	21	3	18	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.56	0.50	0.64	7	1117	8	0	4	4	7
RFA_00664	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	974	16	0	16	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1025	10	1	9	0	14
RFA_00767	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	8	1	6	1	10
RFA_00768	Corona_pk3 links to Rfam database...	0.50	0.44	0.57	8	1877	8	1	5	2	10
RFA_00769	Corona_pk3 links to Rfam database...	0.41	0.44	0.38	8	1932	13	3	10	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.51	0.50	0.53	9	1999	12	2	6	4	9
RFA_00773	Corona_pk3 links to Rfam database...	0.42	0.39	0.47	7	1938	12	1	7	4	11
RFA_00779	Corona_pk3 links to Rfam database...	0.26	0.28	0.26	5	1934	14	6	8	0	13
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	2	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	6	0	4	2	10
RFA_00816	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	23162	66	17	41	8	41
RFA_00817	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	21892	57	12	41	4	41
RFA_00818	R2_retro_el links to Rfam database...	0.25	0.27	0.23	11	20253	51	12	25	14	30
SRP_00241	Plant_SRP links to Rfam database...	0.55	0.60	0.51	49	45959	61	14	34	13	33
SRP_00331	Metazoa_SRP links to Rfam database...	0.61	0.61	0.61	53	37588	49	3	31	15	34
SRP_00340	Metazoa_SRP links to Rfam database...	0.34	0.37	0.33	30	41236	75	10	52	13	52

^top

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 Multilign(seed) - scored higher in this pairwise comparison

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

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

Performance of RNAwolf - scored lower in this pairwise comparison

1. Total counts & total scores for RNAwolf

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