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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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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>Patricio, Mateus</dc:creator>
  <dc:creator>Muffato, Matthieu</dc:creator>
  <dc:creator>Rutherford, Kim Matthew</dc:creator>
  <dc:creator>Gemmell, Neil J.</dc:creator>
  <dc:date>2019-01-24</dc:date>
  <dc:description>This record contains orthology predictions based on the Maker gene annotation
of the tuatara (Sphenodon punctatus) and a set of 25 other species, using the
Ensembl methodology.

See http://doi.org/10.5281/zenodo.1489354 for the Maker annotation in GFF
format.

The files all_trees.emf.gz and all_homologies.tsv.gz contain the phylogenetic
trees (all_trees.emf.gz, in the EMF alignment format) and the derived pairwise
orthologies and paralogies (all_homologies.tsv.gz, in tabular format).

From the phylogenetic trees, sets of 1-to-1 orthologues across all 26 species
were extracted (pure_one2one_orthologies.txt).  Sets of orthologues that span
all the species but include paralogues were reduced to 1 copy per species
using gene order conservation and sequence similarity. This extra dataset is
available in promoted_one2one_orthologies.txt

The main Ensembl entry point for tuatara is:
  http://www.ensembl.org/Sphenodon_punctatus/

This work is supported by Ngatiwai iwi, Allan Wilson Centre, University of
Otago, New Zealand Genomics Limited, Illumina, National eScience
Infrastructure (NeSI NZ).</dc:description>
  <dc:identifier>https://zenodo.org/record/2542571</dc:identifier>
  <dc:identifier>10.5281/zenodo.2542571</dc:identifier>
  <dc:identifier>oai:zenodo.org:2542571</dc:identifier>
  <dc:relation>doi:10.5281/zenodo.2542570</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>tuatara</dc:subject>
  <dc:subject>orthologs</dc:subject>
  <dc:title>Ortholog data from the tuatara genome project</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
</oai_dc:dc>
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