Dataset Open Access

Ortholog data from the tuatara genome project

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

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).

Files (736.3 MB)
Name Size
all_homologies.tsv.gz
md5:0f6c7dcfcdce99ec427d9f44b37ec286
505.4 MB Download
all_trees.emf.gz
md5:642eccde84dd2214d751f6e8af6eac2a
229.4 MB Download
promoted_one2one_orthologies.txt
md5:83ccae6e79688461ca0b58b4791bc124
1.4 MB Download
pure_one2one_orthologies.txt
md5:41972e3fe32f9e0514d935e6a23b620f
58.9 kB Download
README.txt
md5:a52ce250efbda00828a13caf73b193fa
1.1 kB Download
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