January 24, 2019 Dataset Open Access

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

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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.2542571", 
  "author": [
    {
      "family": "Patricio, Mateus"
    }, 
    {
      "family": "Muffato, Matthieu"
    }, 
    {
      "family": "Rutherford, Kim Matthew"
    }, 
    {
      "family": "Gemmell, Neil J."
    }
  ], 
  "issued": {
    "date-parts": [
      [
        2019, 
        1, 
        24
      ]
    ]
  }, 
  "abstract": "<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>", 
  "title": "Ortholog data from the tuatara genome project", 
  "type": "dataset", 
  "id": "2542571"
}