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Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

View ORCID ProfileJaime Huerta-Cepas, View ORCID ProfileKristoffer Forslund, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, View ORCID ProfilePeer Bork
doi: https://doi.org/10.1101/076331
Jaime Huerta-Cepas
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Kristoffer Forslund
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Damian Szklarczyk
2Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
3Bioinformatics/Systems Biology Group, Swiss Institute of Bioinformatics (SIB), Zurich 8057, Switzerland
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Lars Juhl Jensen
4The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen,Copenhagen N 2200, Denmark
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Christian von Mering
2Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
3Bioinformatics/Systems Biology Group, Swiss Institute of Bioinformatics (SIB), Zurich 8057, Switzerland
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Peer Bork
1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
5Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory,Heidelberg 69117, Germany
6Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany
7Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
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  • For correspondence: Email:bork@embl.de
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Abstract

Orthology assignment is ideally suited for functional inference. However, because predicting orthology is computationally intensive at large scale, and most pipelines relatively in accessible, less precise homology-based functional transfer is still the default for (meta-)genome annotation. We therefore developed eggNOG-mapper, a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from eggNOG. To validate our method, we benchmarked Gene Ontology predictions against two widely used homology-based approaches: BLAST and InterProScan. Compared to BLAST, eggNOG-mapper reduced by 7% the rate of false positive assignments, and increased by 19% the ratio of curated terms recovered over all terms assigned per protein. Compared to InterProScan, eggNOG-mapper achieved similar proteome coverage and precision, while predicting on average 32 more terms per protein and increasing by 26% the rate of curated terms recovered over total term assignments per protein. Through strict orthology assignments, eggNOG-mapper further renders more specific annotations than possible from domain similarity only (e.g. predicting gene family names). eggNOG-mapper runs ~15x than BLAST and at least 2.5x faster than InterProScan. The tool is available standalone or as an online service at http://eggnog-mapper.embl.de.

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Posted September 22, 2016.
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Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
Jaime Huerta-Cepas, Kristoffer Forslund, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
bioRxiv 076331; doi: https://doi.org/10.1101/076331
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Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
Jaime Huerta-Cepas, Kristoffer Forslund, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
bioRxiv 076331; doi: https://doi.org/10.1101/076331

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