The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes
Abstract Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online...
Published in: | Nucleic Acids Research |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2022
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Online Access: | https://cea.hal.science/cea-04321536 https://doi.org/10.1093/nar/gkac420 |
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Université d'Évry-Val-d'Essonne: HAL |
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English |
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[SDV]Life Sciences [q-bio] |
spellingShingle |
[SDV]Life Sciences [q-bio] Vernette, Caroline Lecubin, Julien Sánchez, Pablo Acinas, Silvia Babin, Marcel Bork, Peer Boss, Emmanuel Bowler, Chris Cochrane, Guy de Vargas, Colomban Gorsky, Gabriel Guidi, Lionel Grimsley, Nigel Iudicone, Daniele Jaillon, Olivier Kandels-Lewis, Stefanie Karp-Boss, Lee Karsenti, Eric Not, Fabrice Ogata, Hiroyuki Poulton, Nicole Pesant, Stéphane Sardet, Christian Speich, Sabrina Stemmann, Lars Sullivan, Matthew Sunagawa, Shinichi Wincker, Patrick Delmont, Tom Pelletier, Eric Hingamp, Pascal Lescot, Magali The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
Abstract Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/. |
author2 |
Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE) Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche pour le Développement (IRD France-Nord )-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN) Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili Institut méditerranéen d'océanologie (MIO) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS) Centre National de la Recherche Scientifique (CNRS) |
format |
Article in Journal/Newspaper |
author |
Vernette, Caroline Lecubin, Julien Sánchez, Pablo Acinas, Silvia Babin, Marcel Bork, Peer Boss, Emmanuel Bowler, Chris Cochrane, Guy de Vargas, Colomban Gorsky, Gabriel Guidi, Lionel Grimsley, Nigel Iudicone, Daniele Jaillon, Olivier Kandels-Lewis, Stefanie Karp-Boss, Lee Karsenti, Eric Not, Fabrice Ogata, Hiroyuki Poulton, Nicole Pesant, Stéphane Sardet, Christian Speich, Sabrina Stemmann, Lars Sullivan, Matthew Sunagawa, Shinichi Wincker, Patrick Delmont, Tom Pelletier, Eric Hingamp, Pascal Lescot, Magali |
author_facet |
Vernette, Caroline Lecubin, Julien Sánchez, Pablo Acinas, Silvia Babin, Marcel Bork, Peer Boss, Emmanuel Bowler, Chris Cochrane, Guy de Vargas, Colomban Gorsky, Gabriel Guidi, Lionel Grimsley, Nigel Iudicone, Daniele Jaillon, Olivier Kandels-Lewis, Stefanie Karp-Boss, Lee Karsenti, Eric Not, Fabrice Ogata, Hiroyuki Poulton, Nicole Pesant, Stéphane Sardet, Christian Speich, Sabrina Stemmann, Lars Sullivan, Matthew Sunagawa, Shinichi Wincker, Patrick Delmont, Tom Pelletier, Eric Hingamp, Pascal Lescot, Magali |
author_sort |
Vernette, Caroline |
title |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_short |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_full |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_fullStr |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_full_unstemmed |
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
title_sort |
ocean gene atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes |
publisher |
HAL CCSD |
publishDate |
2022 |
url |
https://cea.hal.science/cea-04321536 https://doi.org/10.1093/nar/gkac420 |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://cea.hal.science/cea-04321536 Nucleic Acids Research, 2022, 50 (W1), pp.W516-W526. ⟨10.1093/nar/gkac420⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkac420 cea-04321536 https://cea.hal.science/cea-04321536 doi:10.1093/nar/gkac420 |
op_doi |
https://doi.org/10.1093/nar/gkac420 |
container_title |
Nucleic Acids Research |
container_volume |
50 |
container_issue |
W1 |
container_start_page |
W516 |
op_container_end_page |
W526 |
_version_ |
1786829007476490240 |
spelling |
ftunivevry:oai:HAL:cea-04321536v1 2023-12-31T10:04:04+01:00 The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes Vernette, Caroline Lecubin, Julien Sánchez, Pablo Acinas, Silvia Babin, Marcel Bork, Peer Boss, Emmanuel Bowler, Chris Cochrane, Guy de Vargas, Colomban Gorsky, Gabriel Guidi, Lionel Grimsley, Nigel Iudicone, Daniele Jaillon, Olivier Kandels-Lewis, Stefanie Karp-Boss, Lee Karsenti, Eric Not, Fabrice Ogata, Hiroyuki Poulton, Nicole Pesant, Stéphane Sardet, Christian Speich, Sabrina Stemmann, Lars Sullivan, Matthew Sunagawa, Shinichi Wincker, Patrick Delmont, Tom Pelletier, Eric Hingamp, Pascal Lescot, Magali Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)) Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE) Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE) Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes 2016-2019 (UGA 2016-2019 )-Institut de Recherche pour le Développement (IRD France-Nord )-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN) Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili Institut méditerranéen d'océanologie (MIO) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS) Centre National de la Recherche Scientifique (CNRS) 2022-07-05 https://cea.hal.science/cea-04321536 https://doi.org/10.1093/nar/gkac420 en eng HAL CCSD Oxford University Press info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkac420 cea-04321536 https://cea.hal.science/cea-04321536 doi:10.1093/nar/gkac420 ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://cea.hal.science/cea-04321536 Nucleic Acids Research, 2022, 50 (W1), pp.W516-W526. ⟨10.1093/nar/gkac420⟩ [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2022 ftunivevry https://doi.org/10.1093/nar/gkac420 2023-12-06T17:26:06Z Abstract Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/. Article in Journal/Newspaper Arctic Université d'Évry-Val-d'Essonne: HAL Nucleic Acids Research 50 W1 W516 W526 |