After you have created your own BLAST databases, to make them available in the BLAST AMI, simply copy your BLAST database files onto the instance’s /blast/blastdb_custom directory. E.g.:

scp -i <PATH_TO_YOUR_PEM_OR_SSH_KEY_FILE> <BLASTDB_FILES> ubuntu@<YOUR_INSTANCES_DNS>:/blast/blastdb_custom/

These (and any other) BLAST databases installed in the /blast/blastdb_custom directory in the instance will be immediately available for searching via the URL API, web interface, and BLAST+ command line applications on that instance.

If you run into any difficulty, please feel free to email us at so we can help you!