The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes
International audience 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 ava...
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Online Access: | https://hal.science/hal-03872943 https://doi.org/10.1093/nar/gkac420 |
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ftsorbonneuniv:oai:HAL:hal-03872943v1 2023-05-15T15:09:45+02:00 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 Takuvik International Research Laboratory Université Laval Québec (ULaval)-Centre National de la Recherche Scientifique (CNRS) 2022-07-05 https://hal.science/hal-03872943 https://doi.org/10.1093/nar/gkac420 en eng HAL CCSD Oxford University Press info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkac420 hal-03872943 https://hal.science/hal-03872943 doi:10.1093/nar/gkac420 ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://hal.science/hal-03872943 Nucleic Acids Research, 2022, 50 (W1), pp.W516-W526. ⟨10.1093/nar/gkac420⟩ [SDE.BE]Environmental Sciences/Biodiversity and Ecology info:eu-repo/semantics/article Journal articles 2022 ftsorbonneuniv https://doi.org/10.1093/nar/gkac420 2023-02-07T23:49:59Z International audience 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 HAL Sorbonne Université Arctic Nucleic Acids Research 50 W1 W516 W526 |
institution |
Open Polar |
collection |
HAL Sorbonne Université |
op_collection_id |
ftsorbonneuniv |
language |
English |
topic |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology |
spellingShingle |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology 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 |
[SDE.BE]Environmental Sciences/Biodiversity and Ecology |
description |
International audience 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 |
Takuvik International Research Laboratory Université Laval Québec (ULaval)-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://hal.science/hal-03872943 https://doi.org/10.1093/nar/gkac420 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
ISSN: 0305-1048 EISSN: 1362-4962 Nucleic Acids Research https://hal.science/hal-03872943 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 hal-03872943 https://hal.science/hal-03872943 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_ |
1766340881013538816 |