Dataset Open Access

Ortholog data from the tuatara genome project

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


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    <subfield code="a">&lt;p&gt;This record contains orthology predictions based on the Maker gene annotation&lt;br&gt;
of the tuatara (Sphenodon punctatus) and a set of 25 other species, using the&lt;br&gt;
Ensembl methodology.&lt;/p&gt;

&lt;p&gt;See http://doi.org/10.5281/zenodo.1489354 for the Maker annotation in GFF&lt;br&gt;
format.&lt;/p&gt;

&lt;p&gt;The files all_trees.emf.gz and all_homologies.tsv.gz contain the phylogenetic&lt;br&gt;
trees (all_trees.emf.gz, in the EMF alignment format) and the derived pairwise&lt;br&gt;
orthologies and paralogies (all_homologies.tsv.gz, in tabular format).&lt;/p&gt;

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

&lt;p&gt;The main Ensembl entry point for tuatara is:&lt;br&gt;
&amp;nbsp; http://www.ensembl.org/Sphenodon_punctatus/&lt;/p&gt;

&lt;p&gt;This work is supported by Ngatiwai iwi, Allan Wilson Centre, University of&lt;br&gt;
Otago, New Zealand Genomics Limited, Illumina, National eScience&lt;br&gt;
Infrastructure (NeSI NZ).&lt;/p&gt;</subfield>
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