Ocean Gene Atlas
The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.
Description
More detailed information about this field from each metasource.
The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:00.241008
Webpage:
http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/Webpage
More detailed information about this field from each metasource.
http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:00.241008
Licence:
Name: Not licensedLicence name
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Publications:
Publications
More detailed information about this field from each metasource.
The Ocean Gene Atlas: exploring the biogeography of plankton genes online
PMID: 29788376
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:00.241008
Publications
More detailed information about this field from each metasource.
The Ocean Gene Atlas: exploring the biogeography of plankton genes online
PMID: 29788376
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:00.241008
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The Ocean Gene Atlas: exploring the biogeography of plankton genes online
PubMed citations: 38.
38 articles citing: The Ocean Gene Atlas: exploring the biogeography of plankton genes online
Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220. PMID:35314715
Strategies to access biosynthetic novelty in bacterial genomes for drug discovery. PMID:35296832
Prevalence of Heterotrophic Methylmercury Detoxifying Bacteria across Oceanic Regions. PMID:35245029
Overlooked and widespread pennate diatom-diazotroph symbioses in the sea. PMID:35145076
Functional Characterization of a L-2-Haloacid Dehalogenase From Zobellia galactanivorans DsijT Suggests a Role in Haloacetic Acid Catabolism and a Wide Distribution in Marine Environments. PMID:34621253
Tight Adherence (Tad) Pilus Genes Indicate Putative Niche Differentiation in Phytoplankton Bloom Associated Rhodobacterales. PMID:34447362
Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms. PMID:34408267
Transporter characterisation reveals aminoethylphosphonate mineralisation as a key step in the marine phosphorus redox cycle. PMID:34315891
Metabolic Adaptations to Marine Environments: Molecular Diversity and Evolution of Ovothiol Biosynthesis in Bacteria. PMID:34272861
Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus. PMID:34201869
SPX-related genes regulate phosphorus homeostasis in the marine phytoplankton, Phaeodactylum tricornutum. PMID:34172821
Niche adaptation promoted the evolutionary diversification of tiny ocean predators. PMID:34155140
Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. PMID:34108585
A new family of globally distributed lytic roseophages with unusual deoxythymidine to deoxyuridine substitution. PMID:34033748
A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist. PMID:33891594
Pili allow dominant marine cyanobacteria to avoid sinking and evade predation. PMID:33767153
A novel class of sulfur-containing aminolipids widespread in marine roseobacters. PMID:33750904
Diversity and evolution of bacterial bioluminescence genes in the global ocean. PMID:33575578
N-linked glycosylation enzymes in the diatom Thalassiosira oceanica exhibit a diel cycle in transcript abundance and favor for NXT-type sites. PMID:33547363
A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism. PMID:33536167
Single-Cell Transcriptomics of Abedinium Reveals a New Early-Branching Dinoflagellate Lineage. PMID:33045041
Development of an Ocean Protein Portal for Interactive Discovery and Education. PMID:32897077
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. PMID:32735679
Monogalactosyldiacylglycerol and Sulfolipid Synthesis in Microalgae. PMID:32370033
Exoenzymes as a Signature of Microbial Response to Marine Environmental Conditions. PMID:32291350
A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria. PMID:31941905
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. PMID:31730850
Marine Proteobacteria metabolize glycolate via the β-hydroxyaspartate cycle. PMID:31723261
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Density-dependent oxylipin production in natural diatom communities: possible implications for plankton dynamics. PMID:31611654
Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. PMID:31587637
MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins. PMID:31346176
How haptophytes microalgae mitigate vitamin B12 limitation. PMID:31182768
Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light. PMID:31125464
Marine Natural Products from Microalgae: An -Omics Overview. PMID:31067655
A new widespread subclass of carbonic anhydrase in marine phytoplankton. PMID:31024153
GLOSSary: the GLobal Ocean 16S subunit web accessible resource. PMID:30497362
The chemical cue tetrabromopyrrole induces rapid cellular stress and mortality in phytoplankton. PMID:30341338
Tags:
Tags
More detailed information about this field from each metasource.
ecology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:00.241008
marine biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:00.241008
metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:00.241008
metatranscriptomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:00.241008
Tags
More detailed information about this field from each metasource.
ecology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:00.241008
marine biology
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:00.241008
metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:00.241008
metatranscriptomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:30:00.241008
ecology marine biology metagenomics metatranscriptomics
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