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Publication MIO : Emilie Villar (MIO), Thomas Vannier (MIO), Caroline Vernette (MIO), Magali Lescot (MIO), Miguelangel Cuenca, Aurélien Alexandre (MIO), Paul Bachelerie (MIO), Thomas Rosnet (MIO), Eric Pelletier, Shinichi Sunagawa, Pascal Hingamp (MIO). The Ocean Gene Atlas : exploring the biogeography of plankton genes online, Nucleic Acids Research

Version imprimable de cet article

https://doi.org/10.1093/nar/gky376
Published :
21 May 2018

Article history :
Received : 31 January 2018
Revision Received : : 16 April 2018
Accepted : 02 May 2018

Abstract

The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at : http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.

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