Downloading plant genomes from Biomart

  1. Open a connection to the ensemblgenome server of interest (e.g. http://plants.ensembl.org/).
  2. In the top of the page, click the Biomart link.
  3. Choose database -> Plant Mart.
  4. Choose dataset -> select the species of interest (e.g. Brachypodium).
  5. In the menu on the leftg side, click Attributes.

Download gene coordinates

  1. Create a folder for the genome of interest (for instance biomart_genomes/Brachypodium_distachyon).

  2. Select the gene attributes as in the screenshot below.

gene attributes 2. Before downloading the data, it might be wise to click Count in order to check if the number of features is consistent with your knwoledge of the genome of interest.

  1. Click Results to generate the feature table. Check the preview.

  2. Select Export all results to File in TSV format (tab-separated values).

  3. Think twice to decide whether you need or not unique results.

  4. Click GO.

  5. Save the result in the genome directory created above, and name the file gene.tsv.

Formatting tables for RSAT

export ORG=Brachypodium_distachyon_v1.0
mkdir -p ${RSAT}/public_html/data/genomes/${ORG}/biomart_genome