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(20) - scored lower in this pairwise comparison

Total counts & total scores
Individual counts

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

Overview

Metric	Afold		PPfold(20)
MCC	0.564	>	0.522
Average MCC ± 95% Confidence Intervals	0.638 ± 0.563	>	0.533 ± 0.359
Sensitivity	0.519	>	0.377
Positive Predictive Value	0.618	<	0.727
Total TP	55	>	40
Total TN	16168	<	16202
Total FP	46	>	19
Total FP CONTRA	6	>	0
Total FP INCONS	28	>	15
Total FP COMP	12	>	4
Total FN	51	<	66
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	55
Total TN	16168
Total FP	46
Total FP CONTRA	6
Total FP INCONS	28
Total FP COMP	12
Total FN	51

Total Scores
MCC	0.564
Average MCC ± 95% Confidence Intervals	0.638 ± 0.563
Sensitivity	0.519
Positive Predictive Value	0.618
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
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
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(20) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	40
Total TN	16202
Total FP	19
Total FP CONTRA	0
Total FP INCONS	15
Total FP COMP	4
Total FN	66

Total Scores
MCC	0.522
Average MCC ± 95% Confidence Intervals	0.533 ± 0.359
Sensitivity	0.377
Positive Predictive Value	0.727
Nr of predictions	4

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.63	0.45	0.90	9	980	1	0	1	0	11
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12

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