CompaRNA - on-line benchmarks of RNA structure prediction methods

CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Table of contents:

Overview

Performance Plots

Performance of CRWrnafold - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of RSpredict(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

Compile and download dataset for CRWrnafold & RSpredict(20) [.zip] - may take several seconds...

Overview

Metric	CRWrnafold		RSpredict(20)
MCC	0.546	>	0.446
Average MCC ± 95% Confidence Intervals	0.574 ± 0.189	>	0.452 ± 0.159
Sensitivity	0.483	>	0.331
Positive Predictive Value	0.623	>	0.609
Total TP	114	>	78
Total TN	32629	<	32684
Total FP	81	>	56
Total FP CONTRA	10	>	7
Total FP INCONS	59	>	43
Total FP COMP	12	>	6
Total FN	122	<	158
P-value	0.0

Performance plots

Comparison of performance of CRWrnafold and RSpredict(20). 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 CRWrnafold and RSpredict(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CRWrnafold and RSpredict(20). 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 CRWrnafold and RSpredict(20)).

Performance of CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	114
Total TN	32629
Total FP	81
Total FP CONTRA	10
Total FP INCONS	59
Total FP COMP	12
Total FN	122

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.574 ± 0.189
Sensitivity	0.483
Positive Predictive Value	0.623
Nr of predictions	7

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3SD1_A	THF links to Rfam database...	0.52	0.45	0.61	19	3885	12	2	10	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.13	5	11741	44	4	31	9	28
4AOB_A	SAM links to Rfam database...	0.59	0.48	0.74	20	4344	8	2	5	1	22
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1313	2	1	1	0	8

Performance of RSpredict(20) - scored lower in this pairwise comparison

1. Total counts & total scores for RSpredict(20)

Total Base Pair Counts
Total TP	78
Total TN	32684
Total FP	56
Total FP CONTRA	7
Total FP INCONS	43
Total FP COMP	6
Total FN	158

Total Scores
MCC	0.446
Average MCC ± 95% Confidence Intervals	0.452 ± 0.159
Sensitivity	0.331
Positive Predictive Value	0.609
Nr of predictions	7

2. Individual counts for RSpredict(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.61	0.41	0.92	11	2991	1	0	1	0	16
3SD1_A	THF links to Rfam database...	0.68	0.60	0.78	25	3884	7	1	6	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.33	0.69	18	7114	8	0	8	0	36
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.18	0.20	6	11751	30	6	18	6	27
4AOB_A	SAM links to Rfam database...	0.28	0.14	0.55	6	4360	5	0	5	0	36
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.45	0.32	0.67	6	1317	3	0	3	0	13

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.