Tuesday, 1 February 2022

Exporting protein sequences from Artemis

 I had a gff with the annotation and genome sequences for some contigs, and wanted to export the protein sequences from Artemis. I wrote previously on how to run Artemis here but that was ages ago, so had to remind myself!

To log into the Sanger compute cluster and run Artemis:

% ssh -Y pcs6

% module avail -t | grep -i art

% module load artemis/18.1.0

% art

This then opened Artemis, and to load my gff file, I used the 'File' menu. 

Then to select my genes of interest, I went to the 'View' menu, and choose 'CDS genes and products', and then went to the 'Select' menu and chose 'All CDS features', and chose my genes of interest from the list. Then I went to the 'Write' menu and chose 'Amino acids of selected features to file', and this wrote a file with the protein sequences for my genes of interest. Great!

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