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 Afold - 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 Afold & PPfold(seed) [.zip] - may take several seconds...

Overview

Metric	Afold		PPfold(seed)
MCC	0.489	>	0.187
Average MCC ± 95% Confidence Intervals	0.547 ± 0.441	>	0.137 ± 0.359
Sensitivity	0.443	>	0.066
Positive Predictive Value	0.547	>	0.538
Total TP	47	>	7
Total TN	16721	<	16794
Total FP	52	>	25
Total FP CONTRA	6	>	0
Total FP INCONS	33	>	6
Total FP COMP	13	<	19
Total FN	59	<	99
P-value	0.0

Performance plots

Performance of Afold - scored higher in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	47
Total TN	16721
Total FP	52
Total FP CONTRA	6
Total FP INCONS	33
Total FP COMP	13
Total FN	59

Total Scores
MCC	0.489
Average MCC ± 95% Confidence Intervals	0.547 ± 0.441
Sensitivity	0.443
Positive Predictive Value	0.547
Nr of predictions	4

2. Individual counts for Afold [ 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...	0.61	0.55	0.69	11	1524	6	0	5	1	9
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

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

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

Total Base Pair Counts
Total TP	7
Total TN	16794
Total FP	25
Total FP CONTRA	0
Total FP INCONS	6
Total FP COMP	19
Total FN	99

Total Scores
MCC	0.187
Average MCC ± 95% Confidence Intervals	0.137 ± 0.359
Sensitivity	0.066
Positive Predictive Value	0.538
Nr of predictions	4

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
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	34
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.03	0.20	1	11776	23	0	4	19	32
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19

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