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 Alterna - scored higher in this pairwise comparison

Total counts & total scores
Individual counts

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

Total counts & total scores
Individual counts

Compile and download dataset for Alterna & PPfold(seed) [.zip] - may take several seconds...

Overview

Metric	Alterna		PPfold(seed)
MCC	0.566	>	0.153
Average MCC ± 95% Confidence Intervals	0.567 ± 0.105	>	0.078 ± 0.202
Sensitivity	0.479	>	0.032
Positive Predictive Value	0.679	<	0.750
Total TP	91	>	6
Total TN	16881	<	17007
Total FP	45	>	2
Total FP CONTRA	5	>	0
Total FP INCONS	38	>	2
Total FP COMP	2	>	0
Total FN	99	<	184
P-value	0.0

Performance plots

Performance of Alterna - scored higher in this pairwise comparison

1. Total counts & total scores for Alterna

Total Base Pair Counts
Total TP	91
Total TN	16881
Total FP	45
Total FP CONTRA	5
Total FP INCONS	38
Total FP COMP	2
Total FN	99

Total Scores
MCC	0.566
Average MCC ± 95% Confidence Intervals	0.567 ± 0.105
Sensitivity	0.479
Positive Predictive Value	0.679
Nr of predictions	6

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

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

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

Total Base Pair Counts
Total TP	6
Total TN	17007
Total FP	2
Total FP CONTRA	0
Total FP INCONS	2
Total FP COMP	0
Total FN	184

Total Scores
MCC	0.153
Average MCC ± 95% Confidence Intervals	0.078 ± 0.202
Sensitivity	0.032
Positive Predictive Value	0.750
Nr of predictions	6

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.47	0.30	0.75	6	1532	2	0	2	0	14
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3003	0	0	0	0	27
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2775	0	0	0	0	30
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3570	0	0	0	0	37

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