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Which genome assemblies does GREAT support?

Currently, GREAT supports recent assemblies of the well-annotated human (UCSC hg19 and UCSC hg18), mouse (UCSC mm9) and zebrafish (UCSC danRer7) genomes.

Can I use a different species or assembly?

If you have genomic regions defined for a different species or assembly from the ones we currently support, you can use the UCSC LiftOver utility to convert to a supported assembly. The LiftOver typically works very well for within-species coordinate conversion (e.g. from one human assembly to another), but it can also be used as a best approximation of mapping regions in one genome to the orthologous regions of a genome for a different species (e.g., from chimpanzee to human), although more caution is obviously advised in these cases.

Will you consider expanding GREAT to support additional species?

We do hope to gradually expand the set of species we support. GREAT needs the following to consider adding a new species:

  1. A decent genome assembly.
  2. A decent gene set.
  3. Gene annotations. Typically in the form of an ontology, and gene to ontology term mappings.
  4. A community of researchers actually taking measurements in said species.

For species near enough to human for our own cis-regulation interests - practically all vertebrates - you can help us consider additional species by sending us specific links to rich gene annotation resources unique to your species of interest.

For species more distantly related to human (say fly or arabidopsis) we will likely not do the curation ourselves. However, if you are seriously interested and capable we can consider sharing our file format requirements with you and have you contribute this species into GREAT.

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