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Ortholog data from the tuatara genome project

Patricio, Mateus; Muffato, Matthieu; Rutherford, Kim Matthew; Gemmell, Neil J.


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{
  "description": "<p>This record contains orthology predictions based on the Maker gene annotation<br>\nof the tuatara (Sphenodon punctatus) and a set of 25 other species, using the<br>\nEnsembl methodology.</p>\n\n<p>See http://doi.org/10.5281/zenodo.1489354 for the Maker annotation in GFF<br>\nformat.</p>\n\n<p>The files all_trees.emf.gz and all_homologies.tsv.gz contain the phylogenetic<br>\ntrees (all_trees.emf.gz, in the EMF alignment format) and the derived pairwise<br>\northologies and paralogies (all_homologies.tsv.gz, in tabular format).</p>\n\n<p>From the phylogenetic trees, sets of 1-to-1 orthologues across all 26 species<br>\nwere extracted (pure_one2one_orthologies.txt).&nbsp; Sets of orthologues that span<br>\nall the species but include paralogues were reduced to 1 copy per species<br>\nusing gene order conservation and sequence similarity. This extra dataset is<br>\navailable in promoted_one2one_orthologies.txt</p>\n\n<p>The main Ensembl entry point for tuatara is:<br>\n&nbsp; http://www.ensembl.org/Sphenodon_punctatus/</p>\n\n<p>This work is supported by Ngatiwai iwi, Allan Wilson Centre, University of<br>\nOtago, New Zealand Genomics Limited, Illumina, National eScience<br>\nInfrastructure (NeSI NZ).</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "European Bioinformatics Institute", 
      "@id": "https://orcid.org/0000-0003-2056-3946", 
      "@type": "Person", 
      "name": "Patricio, Mateus"
    }, 
    {
      "affiliation": "European Bioinformatics Institute", 
      "@id": "https://orcid.org/0000-0002-7860-3560", 
      "@type": "Person", 
      "name": "Muffato, Matthieu"
    }, 
    {
      "affiliation": "University of Cambridge", 
      "@id": "https://orcid.org/0000-0001-6277-726X", 
      "@type": "Person", 
      "name": "Rutherford, Kim Matthew"
    }, 
    {
      "affiliation": "University of Otago", 
      "@id": "https://orcid.org/0000-0003-0671-3637", 
      "@type": "Person", 
      "name": "Gemmell, Neil J."
    }
  ], 
  "url": "https://zenodo.org/record/2542571", 
  "datePublished": "2019-01-24", 
  "keywords": [
    "tuatara", 
    "orthologs"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/b91db622-7fd0-444f-9aea-e4ac982db958/all_homologies.tsv.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/b91db622-7fd0-444f-9aea-e4ac982db958/all_trees.emf.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/b91db622-7fd0-444f-9aea-e4ac982db958/promoted_one2one_orthologies.txt", 
      "encodingFormat": "txt", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/b91db622-7fd0-444f-9aea-e4ac982db958/pure_one2one_orthologies.txt", 
      "encodingFormat": "txt", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/b91db622-7fd0-444f-9aea-e4ac982db958/README.txt", 
      "encodingFormat": "txt", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.2542571", 
  "@id": "https://doi.org/10.5281/zenodo.2542571", 
  "@type": "Dataset", 
  "name": "Ortholog data from the tuatara genome project"
}
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