eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Centro de Biotecnología y Genómica de Plantas (CBGP)

Bibliographic Details
Authors: Cantalapiedra, Carlos P, Hernández-Plaza, Ana, Letunic, Ivica, Bork, Peer, Huerta-Cepas, Jaime
Format: article
Status:Published version
Publication Date:2021
Country:España
Institution:Consejo Superior de Investigaciones Científicas (CSIC)
Repository:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/275217
Online Access:http://hdl.handle.net/10261/275217
https://api.elsevier.com/content/abstract/scopus_id/85118367784
Access Level:Open access
Keyword:Bioinformatics
Computational genomics
Functional annotation
Metagenomics
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spelling eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic ScaleCantalapiedra, Carlos PHernández-Plaza, AnaLetunic, IvicaBork, PeerHuerta-Cepas, JaimeBioinformaticsComputational genomicsFunctional annotationMetagenomicsCentro de Biotecnología y Genómica de Plantas (CBGP)Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.This research was supported by the National Programme for Fostering Excellence in Scientific and Technical Research (Grant No. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE, to J.H.C.) and the Severo Ochoa Centres of Excellence Programme (Grant No. SEV-2016-0672 (2017–2021) to C.P.C.) from the State Research Agency (AEI) of Spain, as well as a Research Technical Support Staff Aid (PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.); European Research Council grant MicroBioS (ERC-2014-AdG)—GA669830 (to P.B.). Cloud computing is supported by BMBF (de.NBI network #031A537B).Peer reviewed5 Pág.Oxford University PressAgencia Estatal de Investigación (España)European CommissionCantalapiedra, Carlos P [0000-0001-5263-533X]Hernández-Plaza, Ana [0000-0002-9844-7999]Letunic, Ivica [0000-0003-3560-4288]Bork, Peer [0000-0002-2627-833X]Huerta-Cepas, Jaime [0000-0003-4195-5025]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202220222021info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/275217https://api.elsevier.com/content/abstract/scopus_id/85118367784reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-098073-A-I00info:eu-repo/grantAgreement/AEI/SEV-2016-0672 (2017–2021)/info:eu-repo/grantAgreement/EC/ERC-2014-AdG)—GA669830 (a P.B.)./Molecular biology and evolutionhttps://doi.org/10.1093/molbev/msab293Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2752172026-05-22T06:33:51Z
dc.title.none.fl_str_mv eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
title eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
spellingShingle eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
Cantalapiedra, Carlos P
Bioinformatics
Computational genomics
Functional annotation
Metagenomics
title_short eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
title_full eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
title_fullStr eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
title_full_unstemmed eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
title_sort eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
dc.creator.none.fl_str_mv Cantalapiedra, Carlos P
Hernández-Plaza, Ana
Letunic, Ivica
Bork, Peer
Huerta-Cepas, Jaime
author Cantalapiedra, Carlos P
author_facet Cantalapiedra, Carlos P
Hernández-Plaza, Ana
Letunic, Ivica
Bork, Peer
Huerta-Cepas, Jaime
author_role author
author2 Hernández-Plaza, Ana
Letunic, Ivica
Bork, Peer
Huerta-Cepas, Jaime
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Agencia Estatal de Investigación (España)
European Commission
Cantalapiedra, Carlos P [0000-0001-5263-533X]
Hernández-Plaza, Ana [0000-0002-9844-7999]
Letunic, Ivica [0000-0003-3560-4288]
Bork, Peer [0000-0002-2627-833X]
Huerta-Cepas, Jaime [0000-0003-4195-5025]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Bioinformatics
Computational genomics
Functional annotation
Metagenomics
topic Bioinformatics
Computational genomics
Functional annotation
Metagenomics
description Centro de Biotecnología y Genómica de Plantas (CBGP)
publishDate 2021
dc.date.none.fl_str_mv 2021
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/275217
https://api.elsevier.com/content/abstract/scopus_id/85118367784
url http://hdl.handle.net/10261/275217
https://api.elsevier.com/content/abstract/scopus_id/85118367784
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-098073-A-I00
info:eu-repo/grantAgreement/AEI/SEV-2016-0672 (2017–2021)/
info:eu-repo/grantAgreement/EC/ERC-2014-AdG)—GA669830 (a P.B.)./
Molecular biology and evolution
https://doi.org/10.1093/molbev/msab293
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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