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/.
Highlights
Marine plankton provide essential ecosystemic functions on the planet: at the basis of the ocean food web, they contribute about half of global primary production [1]
The Marine Atlas of Tara Oceans Unigenes (MATOU) is a catalog of 116 million unigenes
Users can search for sequences similar to their query in either one of two marine gene catalogues (Figure 1B): the Ocean Microbial Reference Gene Catalog (OM-RGC) [8] or the MATOU [9]
Summary
Marine plankton provide essential ecosystemic functions on the planet: at the basis of the ocean food web, they contribute about half of global primary production [1]. The Ocean Gene Atlas (OGA) web service provides a submission interface to collect a nucleic or protein sequence query, it executes data mining procedures on dedicated high performance hardware, and returns interactive result panels for data exploration (Figure 1).
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