The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.

Autor:	Vernette C; Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.; Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France., Lecubin J; SIP, OSU PYTHEAS, Marseille, France., Sánchez P; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain., Sunagawa S; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland., Delmont TO; Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France.; Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91057 Evry, France., Acinas SG; Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain., Pelletier E; Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France.; Génomique Métabolique, Genoscope, Institut de Biologie François-Jacob, CEA, CNRS, Univ Evry, Univ Paris-Saclay, 91057 Evry, France., Hingamp P; Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France., Lescot M; Aix-Marseille Université, Université de Toulon, IRD, CNRS, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France.; Research Federation for the study of Global Ocean systems ecology and evolution, FR2022/Tara Oceans-GOSEE, Paris, France.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2022 Jul 05; Vol. 50 (W1), pp. W516-W526.
DOI:	10.1093/nar/gkac420
Abstrakt:	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/. (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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