EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods

We want to acknowledge Joel Moro for his help in the analysis of the protist dataset and Daniel Majer for his help with the web interface. TG group acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by European Regional Development Fund...

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Autores: Marcet-Houben, Marina, Collado Cala, Ismael, Fuentes Palacios, Diego, Gómez, Alicia D., Molina, Manuel, Garisoain, Andrés, Chorostecki, Uciel Pablo, Gabaldón, Toni
Tipo de documento: artigo
Data de publicação:2023
País:España
Recursos:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositório:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:20.500.12328/4783
Acesso em linha:http://hdl.handle.net/20.500.12328/4783
https://dx.doi.org/10.1016/j.jmb.2023.168013
Access Level:Acceso aberto
Palavra-chave:Ordre dels gens
Genòmica comparada
Servidor web
Eucariotes
Barri de gens
Orden de genes
Genómica comparativa
Eucariotas
Vecindario de genes
Gene order
Comparative genomics
Web server
Eukaryotes
Gene neighbourhood
57
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spelling EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoodsMarcet-Houben, MarinaCollado Cala, IsmaelFuentes Palacios, DiegoGómez, Alicia D.Molina, ManuelGarisoain, AndrésChorostecki, Uciel PabloGabaldón, ToniOrdre dels gensGenòmica comparadaServidor webEucariotesBarri de gensOrden de genesGenómica comparativaServidor webEucariotasVecindario de genesGene orderComparative genomicsWeb serverEukaryotesGene neighbourhood57We want to acknowledge Joel Moro for his help in the analysis of the protist dataset and Daniel Majer for his help with the web interface. TG group acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by European Regional Development Fund (ERDF); from the Catalan Research Agency (AGAUR) SGR423; from the European Union’s Horizon 2020 research and innovation programme (ERC-2016-724173); from the Gordon and Betty Moore Foundation (Grant GBMF9742); from the “La Caixa” foundation (Grant LCF/PR/HR21/00737), and from the Instituto de Salud Carlos III (IMPACT Grant IMP/00019 and CIBERINFEC CB21/13/00061- ISCIII-SGEFI/ERDF). UC was funded in part through H2020 Marie Skłodowska-Curie Actions (H2020-MSCA-IF-2017-793699) and MICINN (IJC2019-039402-I).Conservation of gene neighbourhood over evolutionary distances is generally indicative of shared regulation or functional association among genes. This concept has been broadly exploited in prokaryotes but its use on eukaryotic genomes has been limited to specific functional classes, such as biosynthetic gene clusters. We here used an evolutionary-based gene cluster discovery algorithm (EvolClust) to pre-compute evolutionarily conserved gene neighbourhoods, which can be searched, browsed and downloaded in EvolClustDB. We inferred ∼35,000 cluster families in 882 different species in genome comparisons of five taxonomically broad clades: Fungi, Plants, Metazoans, Insects and Protists. EvolClustDB allows browsing through the cluster families, as well as searching by protein, species, identifier or sequence. Visualization allows inspecting gene order per species in a phylogenetic context, so that relevant evolutionary events such as gain, loss or transfer, can be inferred. EvolClustDB is freely available, without registration, at http://evolclustdb.org/.info:eu-repo/semantics/publishedVersionElsevier2023info:eu-repo/semantics/article7http://hdl.handle.net/20.500.12328/4783https://dx.doi.org/10.1016/j.jmb.2023.168013reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésJournal of Molecular Biology435;14info:eu-repo/grantAgreement/EC/H2020/724173info:eu-repo/grantAgreement/EC/H2020/793699info:eu-repo/grantAgreement/ES/MICINN/IJC2019-039402-IUnder a Creative Commons license.https://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:20.500.12328/47832026-05-29T05:05:01Z
dc.title.none.fl_str_mv EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
title EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
spellingShingle EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
Marcet-Houben, Marina
Ordre dels gens
Genòmica comparada
Servidor web
Eucariotes
Barri de gens
Orden de genes
Genómica comparativa
Servidor web
Eucariotas
Vecindario de genes
Gene order
Comparative genomics
Web server
Eukaryotes
Gene neighbourhood
57
title_short EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
title_full EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
title_fullStr EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
title_full_unstemmed EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
title_sort EvolClustDB: exploring eukaryotic gene clusters with evolutionarily conserved genomic neighbourhoods
dc.creator.none.fl_str_mv Marcet-Houben, Marina
Collado Cala, Ismael
Fuentes Palacios, Diego
Gómez, Alicia D.
Molina, Manuel
Garisoain, Andrés
Chorostecki, Uciel Pablo
Gabaldón, Toni
author Marcet-Houben, Marina
author_facet Marcet-Houben, Marina
Collado Cala, Ismael
Fuentes Palacios, Diego
Gómez, Alicia D.
Molina, Manuel
Garisoain, Andrés
Chorostecki, Uciel Pablo
Gabaldón, Toni
author_role author
author2 Collado Cala, Ismael
Fuentes Palacios, Diego
Gómez, Alicia D.
Molina, Manuel
Garisoain, Andrés
Chorostecki, Uciel Pablo
Gabaldón, Toni
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ordre dels gens
Genòmica comparada
Servidor web
Eucariotes
Barri de gens
Orden de genes
Genómica comparativa
Servidor web
Eucariotas
Vecindario de genes
Gene order
Comparative genomics
Web server
Eukaryotes
Gene neighbourhood
57
topic Ordre dels gens
Genòmica comparada
Servidor web
Eucariotes
Barri de gens
Orden de genes
Genómica comparativa
Servidor web
Eucariotas
Vecindario de genes
Gene order
Comparative genomics
Web server
Eukaryotes
Gene neighbourhood
57
description We want to acknowledge Joel Moro for his help in the analysis of the protist dataset and Daniel Majer for his help with the web interface. TG group acknowledges support from the Spanish Ministry of Science and Innovation for grant PGC2018-099921-B-I00, cofounded by European Regional Development Fund (ERDF); from the Catalan Research Agency (AGAUR) SGR423; from the European Union’s Horizon 2020 research and innovation programme (ERC-2016-724173); from the Gordon and Betty Moore Foundation (Grant GBMF9742); from the “La Caixa” foundation (Grant LCF/PR/HR21/00737), and from the Instituto de Salud Carlos III (IMPACT Grant IMP/00019 and CIBERINFEC CB21/13/00061- ISCIII-SGEFI/ERDF). UC was funded in part through H2020 Marie Skłodowska-Curie Actions (H2020-MSCA-IF-2017-793699) and MICINN (IJC2019-039402-I).
publishDate 2023
dc.date.none.fl_str_mv 2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12328/4783
https://dx.doi.org/10.1016/j.jmb.2023.168013
url http://hdl.handle.net/20.500.12328/4783
https://dx.doi.org/10.1016/j.jmb.2023.168013
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Journal of Molecular Biology
435;14
info:eu-repo/grantAgreement/EC/H2020/724173
info:eu-repo/grantAgreement/EC/H2020/793699
info:eu-repo/grantAgreement/ES/MICINN/IJC2019-039402-I
dc.rights.none.fl_str_mv Under a Creative Commons license.
https://creativecommons.org/licenses/by-nc/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Under a Creative Commons license.
https://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 7
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.223283

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