CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	RNAalifold(seed)		Murlet(seed)
MCC	0.758	>	0.569
Average MCC ± 95% Confidence Intervals	0.761 ± 0.056	>	0.550 ± 0.089
Sensitivity	0.635	>	0.383
Positive Predictive Value	0.904	>	0.845
Total TP	1657	>	1000
Total TN	1503598	<	1504247
Total FP	280	>	241
Total FP CONTRA	17	>	15
Total FP INCONS	159	<	169
Total FP COMP	104	>	57
Total FN	951	<	1608
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of RNAalifold(seed) and Murlet(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 RNAalifold(seed) and Murlet(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 RNAalifold(seed) and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and Murlet(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 RNAalifold(seed) and Murlet(seed)).

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

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

Total Base Pair Counts
Total TP	1657
Total TN	1503598
Total FP	280
Total FP CONTRA	17
Total FP INCONS	159
Total FP COMP	104
Total FN	951

Total Scores
MCC	0.758
Average MCC ± 95% Confidence Intervals	0.761 ± 0.056
Sensitivity	0.635
Positive Predictive Value	0.904
Nr of predictions	31

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00606	Telomerase-cil links to Rfam database...	0.89	0.79	1.00	31	21290	0	0	0	0	8
RFA_00620	Telomerase-cil links to Rfam database...	0.88	0.77	1.00	30	21915	0	0	0	0	9
RFA_00626	rne5 links to Rfam database...	0.97	0.94	1.00	82	56534	6	0	0	6	5
RFA_00627	rne5 links to Rfam database...	0.96	0.93	1.00	81	56872	7	0	0	7	6
RFA_00628	rne5 links to Rfam database...	0.97	0.94	1.00	81	57210	6	0	0	6	5
RFA_00630	rne5 links to Rfam database...	0.92	0.87	0.96	76	56874	12	0	3	9	11
RFA_00639	7SK links to Rfam database...	0.22	0.14	0.36	12	54582	21	4	17	0	75
RFA_00814	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	25172	0	0	0	0	13
RFA_00815	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	24503	0	0	0	0	13
RFA_00816	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	23192	0	0	0	0	13
RFA_00817	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	21917	0	0	0	0	13
RFA_00818	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	20273	0	0	0	0	13
RFA_00819	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	27938	0	0	0	0	13
RFA_00820	bicoid_3 links to Rfam database...	0.80	0.68	0.95	109	151410	7	0	6	1	51
RFA_00830	bicoid_3 links to Rfam database...	0.66	0.54	0.81	83	152525	21	0	20	1	71
SRP_00079	Plant_SRP links to Rfam database...	0.63	0.50	0.80	44	41850	15	0	11	4	44
SRP_00124	Metazoa_SRP links to Rfam database...	0.63	0.46	0.87	39	37083	15	2	4	9	46
SRP_00182	Plant_SRP links to Rfam database...	0.73	0.55	0.95	56	45997	4	0	3	1	45
SRP_00197	Archaea_SRP links to Rfam database...	0.83	0.72	0.96	73	49379	8	0	3	5	28
SRP_00198	Archaea_SRP links to Rfam database...	0.82	0.71	0.96	73	50964	8	0	3	5	30
SRP_00199	Archaea_SRP links to Rfam database...	0.82	0.70	0.96	73	50964	8	0	3	5	32
SRP_00202	Archaea_SRP links to Rfam database...	0.78	0.64	0.96	75	54207	4	0	3	1	42
SRP_00241	Plant_SRP links to Rfam database...	0.59	0.48	0.72	39	46002	22	4	11	7	43
SRP_00255	Archaea_SRP links to Rfam database...	0.74	0.66	0.84	62	47512	18	0	12	6	32
SRP_00260	Metazoa_SRP links to Rfam database...	0.54	0.44	0.66	44	47828	27	4	19	4	56
SRP_00278	Archaea_SRP links to Rfam database...	0.77	0.65	0.91	68	45981	9	0	7	2	37
SRP_00322	Archaea_SRP links to Rfam database...	0.78	0.65	0.93	71	48440	7	0	5	2	38
SRP_00328	Metazoa_SRP links to Rfam database...	0.64	0.48	0.85	41	39573	11	1	6	4	44
SRP_00329	Metazoa_SRP links to Rfam database...	0.66	0.51	0.86	43	39853	14	0	7	7	42
SRP_00339	Archaea_SRP links to Rfam database...	0.79	0.69	0.90	65	44479	10	0	7	3	29
SRP_00340	Metazoa_SRP links to Rfam database...	0.60	0.46	0.78	38	41279	20	2	9	9	44

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

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

Total Base Pair Counts
Total TP	1000
Total TN	1504247
Total FP	241
Total FP CONTRA	15
Total FP INCONS	169
Total FP COMP	57
Total FN	1608

Total Scores
MCC	0.569
Average MCC ± 95% Confidence Intervals	0.550 ± 0.089
Sensitivity	0.383
Positive Predictive Value	0.845
Nr of predictions	31

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
RFA_00606	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	21321	0	0	0	0	39
RFA_00620	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	21945	0	0	0	0	39
RFA_00626	rne5 links to Rfam database...	0.81	0.66	1.00	57	56559	4	0	0	4	30
RFA_00627	rne5 links to Rfam database...	0.84	0.70	1.00	61	56892	5	0	0	5	26
RFA_00628	rne5 links to Rfam database...	0.83	0.69	1.00	59	57232	8	0	0	8	27
RFA_00630	rne5 links to Rfam database...	0.82	0.67	1.00	58	56895	4	0	0	4	29
RFA_00639	7SK links to Rfam database...	0.21	0.11	0.40	10	54590	15	4	11	0	77
RFA_00814	R2_retro_el links to Rfam database...	0.75	0.63	0.90	26	25171	4	0	3	1	15
RFA_00815	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	24503	1	0	0	1	13
RFA_00816	R2_retro_el links to Rfam database...	0.75	0.63	0.90	26	23191	4	0	3	1	15
RFA_00817	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	21917	1	0	0	1	13
RFA_00818	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	20273	1	0	0	1	13
RFA_00819	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	27938	0	0	0	0	13
RFA_00820	bicoid_3 links to Rfam database...	0.71	0.56	0.89	90	151424	13	3	8	2	70
RFA_00830	bicoid_3 links to Rfam database...	0.59	0.45	0.78	70	152538	23	3	17	3	84
SRP_00079	Plant_SRP links to Rfam database...	0.54	0.33	0.88	29	41872	6	0	4	2	59
SRP_00124	Metazoa_SRP links to Rfam database...	0.15	0.09	0.24	8	37094	27	3	23	1	77
SRP_00182	Plant_SRP links to Rfam database...	0.59	0.35	1.00	35	46021	1	0	0	1	66
SRP_00197	Archaea_SRP links to Rfam database...	0.47	0.28	0.80	28	49420	8	0	7	1	73
SRP_00198	Archaea_SRP links to Rfam database...	0.47	0.27	0.82	28	51006	7	0	6	1	75
SRP_00199	Archaea_SRP links to Rfam database...	0.47	0.24	0.93	25	51013	3	0	2	1	80
SRP_00202	Archaea_SRP links to Rfam database...	0.48	0.25	0.94	29	54254	2	0	2	0	88
SRP_00241	Plant_SRP links to Rfam database...	0.51	0.33	0.79	27	46022	9	0	7	2	55
SRP_00255	Archaea_SRP links to Rfam database...	0.65	0.43	1.00	40	47546	2	0	0	2	54
SRP_00260	Metazoa_SRP links to Rfam database...	0.21	0.14	0.33	14	47852	29	1	28	0	86
SRP_00278	Archaea_SRP links to Rfam database...	0.53	0.30	0.94	31	46023	3	0	2	1	74
SRP_00322	Archaea_SRP links to Rfam database...	0.44	0.25	0.79	27	48482	8	0	7	1	82
SRP_00328	Metazoa_SRP links to Rfam database...	0.49	0.34	0.71	29	39580	16	1	11	4	56
SRP_00329	Metazoa_SRP links to Rfam database...	0.50	0.34	0.73	29	39863	16	0	11	5	56
SRP_00339	Archaea_SRP links to Rfam database...	0.49	0.32	0.77	30	44512	9	0	9	0	64
SRP_00340	Metazoa_SRP links to Rfam database...	0.44	0.27	0.73	22	41298	12	0	8	4	60

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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 RNAalifold(seed) - scored higher in this pairwise comparison

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

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

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

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

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