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 Mastr(20) - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

Performance of CRWrnafold - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Mastr(20)		CRWrnafold
MCC	0.547	>	0.546
Average MCC ± 95% Confidence Intervals	0.482 ± 0.238	<	0.574 ± 0.189
Sensitivity	0.373	<	0.483
Positive Predictive Value	0.807	>	0.623
Total TP	88	<	114
Total TN	32703	>	32629
Total FP	24	<	81
Total FP CONTRA	1	<	10
Total FP INCONS	20	<	59
Total FP COMP	3	<	12
Total FN	148	>	122
P-value	0.0

Performance plots

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

Performance of Mastr(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	88
Total TN	32703
Total FP	24
Total FP CONTRA	1
Total FP INCONS	20
Total FP COMP	3
Total FN	148

Total Scores
MCC	0.547
Average MCC ± 95% Confidence Intervals	0.482 ± 0.238
Sensitivity	0.373
Positive Predictive Value	0.807
Nr of predictions	7

2. Individual counts for Mastr(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...	0.77	0.59	1.00	16	2987	1	0	0	1	11
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	7	0	6	1	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4AOB_A	SAM links to Rfam database...	0.39	0.26	0.58	11	4352	9	0	8	1	31
4ENB_A	crcB links to Rfam database...	0.39	0.16	1.00	3	1272	0	0	0	0	16
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

Performance of CRWrnafold - scored lower 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

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