Build a local index with makeblastdb — getting -dbtype nucl or prot right is what makes it work — then version it, checksum it, and pack a tarball for S3.

Build a local BLAST database from a source FASTA so searches can run against it without sending data to NCBI. Getting -dbtype right (nucl vs. prot) is what determines whether the index works — it must match the sequences you're indexing and the search program you'll run.

Where these commands run

You cannot open a shell on the platform yourself. The commands on this page are BLAST+ command lines: ask Ivy in chat to run them in the chat's code workspace, which ships BLAST+, or run them on your own machine. For a hosted search with no commands, see the BLAST quickstart.

Build a database

makeblastdb \
  -in inputs/db/source.fasta \
  -dbtype nucl \
  -parse_seqids \
  -out inputs/db/genomes_v1

For protein:

makeblastdb -in inputs/db/source_prot.fasta -dbtype prot -out inputs/db/proteins_v1

Versioning pattern

Keep databases under inputs/db/<name>_<version>/.
Store the source FASTA alongside the generated index files.
Record MD5 checksums in inputs/db/<name>_<version>/CHECKSUMS.txt.

cd inputs/db
md5sum genomes_v1.* > genomes_v1/CHECKSUMS.txt

Packing for S3

tar -czf outputs/genomes_v1.tar.gz -C inputs/db genomes_v1*

Keep the tarball and restore it wherever you run BLAST, to avoid rebuilding each run.

Refresh cadence

Public databases: refresh weekly or monthly depending on size.
Internal databases: refresh on source data updates; bump the version suffix and update CHECKSUMS.

Local database prep

Build a database

Versioning pattern

Packing for S3

Refresh cadence

On this page