eggNOG v4.0: nested orthology inference across 3686 organisms

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• dc.contributor.author Powell, Seanca
• dc.contributor.author Forslund, Kristofferca
• dc.contributor.author Szklarczyk, Damianca
• dc.contributor.author Trachana, Kalliopica
• dc.contributor.author Roth, Alexanderca
• dc.contributor.author Huerta Cepas, Jaimeca
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-ca
• dc.contributor.author Rattei, Thomasca
• dc.contributor.author Creevey, Chrisca
• dc.contributor.author Kuhn, Michaelca
• dc.contributor.author Jensen, Lars J.ca
• dc.contributor.author Mering, Christian vonca
• dc.contributor.author Bork, Peerca
• dc.date.accessioned 2014-05-14T07:34:22Z
• dc.date.available 2014-05-14T07:34:22Z
• dc.date.issued 2014ca
• dc.description.abstract With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.
• dc.description.sponsorship This work was supported by ERC [UMICIS/242870]; Spanish Juan de la Cierva postdoctoral program [JCI2010-07614]; Jose Castillejo/nmobility program [CAS12/00357]; Alexander von Humboldt Foundation; Novo Nordisk Foundation Center for Protein Research. Funding for access open access charge: EMBL internal budget
• dc.format.mimetype application/pdfca
• dc.identifier.citation Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 2014;42(1):D231-D239. DOI: 10.1093/nar/gkt1253ca
• dc.identifier.doi http://dx.doi.org/10.1093/nar/gkt1253
• dc.identifier.issn 0305-1048ca
• dc.identifier.uri http://hdl.handle.net/10230/22486
• dc.language.iso engca
• dc.publisher Oxford University Pressca
• dc.relation.ispartof Nucleic Acids Research. 2014;42(1):D231-D239
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/242870ca
• dc.rights © 2013 Sean Powell et al. This is an Open Acces article distributed under a Creative Commons Attribution Non-Commercial Licenseca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/3.0/
• dc.subject.other Genètica
• dc.subject.other Genòmica
• dc.subject.other Filogènia
• dc.title eggNOG v4.0: nested orthology inference across 3686 organismsca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca