title: eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
abstract: eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes to the algorithm for creating OGs across taxonomic levels, making nested groups hierarchically consistent. This allows for a better propagation of functional terms across nested OGs and led to the novel annotation of 95 890 previously uncharacterized OGs, increasing overall annotation coverage from 67% to 72%. The functional annotations of OGs have been expanded to also provide Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group. Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of phylogenetic trees. We have also incorporated a framework for quickly mapping novel sequences to OGs based on precomputed HMM profiles. Finally, eggNOG version 4.5 incorporates a novel data set spanning 2605 viral OGs, covering 5228 proteins from 352 viral proteomes. All data are accessible for bulk downloading, as a web-service, and through a completely redesigned web interface. The new access points provide faster searches and a number of new browsing and visualization capabilities, facilitating the needs of both experts and less experienced users. eggNOG v4.5 is available at http://eggnog.embl.de.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland Bioinformatics/Systems Biology Group, Swiss Institute of Bioinformatics (SIB), Zurich 8057, Switzerland.
authors.forename: Damian
authors.initials: D
authors.lastname: Szklarczyk
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Forslund
authors.affiliation: The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N 2200, Denmark.
authors.forename: Helen
authors.initials: H
authors.lastname: Cook
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland Bioinformatics/Systems Biology Group, Swiss Institute of Bioinformatics (SIB), Zurich 8057, Switzerland.
authors.forename: Davide
authors.initials: D
authors.lastname: Heller
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg 85764, Germany.
authors.forename: Mathias C
authors.initials: MC
authors.lastname: Walter
authors.affiliation: CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna 1090, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.affiliation: Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI 96822, USA.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Mende
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Kuhn
authors.affiliation: The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N 2200, Denmark.
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.affiliation: Institute of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland Bioinformatics/Systems Biology Group, Swiss Institute of Bioinformatics (SIB), Zurich 8057, Switzerland mering@imls.uzh.ch.
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg 69117, Germany Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany bork@embl.de.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000465:Algorithms; D019843:Archaeal Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D030562:Databases, Protein; D056890:Eukaryota; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020543:Proteome / Q000737:chemistry; D020539:Sequence Analysis, Protein; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D020543:Proteome; D014764:Viral Proteins