CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Multilign(seed)		ProbKnot
MCC	0.681	>	0.566
Average MCC ± 95% Confidence Intervals	0.547 ± 0.131	>	0.526 ± 0.106
Sensitivity	0.649	>	0.578
Positive Predictive Value	0.717	>	0.556
Total TP	576	>	513
Total TN	406244	>	406125
Total FP	315	<	528
Total FP CONTRA	48	<	107
Total FP INCONS	179	<	302
Total FP COMP	88	<	119
Total FN	312	<	375
P-value	5.02343278931e-08

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Performance plots

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

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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

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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

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Performance of ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	513
Total TN	406125
Total FP	528
Total FP CONTRA	107
Total FP INCONS	302
Total FP COMP	119
Total FN	375

Total Scores
MCC	0.566
Average MCC ± 95% Confidence Intervals	0.526 ± 0.106
Sensitivity	0.578
Positive Predictive Value	0.556
Nr of predictions	23

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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
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00619	-	0.28	0.33	0.24	13	22737	57	13	28	16	26
RFA_00626	rne5 links to Rfam database...	0.86	0.80	0.91	70	56539	32	1	6	25	17
RFA_00628	rne5 links to Rfam database...	0.90	0.88	0.93	76	57209	31	1	5	25	10
RFA_00630	rne5 links to Rfam database...	0.69	0.66	0.72	57	56874	41	4	18	19	30
RFA_00654	Vimentin3 links to Rfam database...	0.23	0.22	0.25	4	2399	12	2	10	0	14
RFA_00658	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	5	0	3	2	7
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.33	0.29	0.40	4	1025	6	0	6	0	10
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
RFA_00816	R2_retro_el links to Rfam database...	0.80	0.88	0.73	36	23171	20	9	4	7	5
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21883	57	18	39	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.48	0.54	0.43	22	20250	38	13	16	9	19
SRP_00241	Plant_SRP links to Rfam database...	0.44	0.48	0.41	39	45960	60	17	40	3	43
SRP_00331	Metazoa_SRP links to Rfam database...	0.54	0.54	0.55	47	37589	42	7	32	3	40
SRP_00340	Metazoa_SRP links to Rfam database...	0.51	0.55	0.47	45	41232	53	10	41	2	37

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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 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 ProbKnot - scored lower in this pairwise comparison

1. Total counts & total scores for ProbKnot

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