Limiting search by taxonomy

To limit a BLAST search by taxonomy, one needs to provide the NCBI taxonomy ID(s) (taxid) for given taxonomic group(s). A taxid is simply a number that specifies a node in the taxonomic tree.

Taxids can be provided to ElasticBLAST using BLAST command-line options (see BLAST options):

  1. -taxids with comma-separated list of taxids, or

  2. -taxidlist with a path to a file that contains a list of taxids, one per line. This file must be present in the local file system where ElasticBLAST is run. Cloud storage locations, like s3:// or gs:// will not work.

ElasticBLAST accepts taxids of any rank.

You can read more about limiting search by taxonomy in command line BLAST+ tools here.


Below is an example ElasticBLAST configuration file that limits search results by taxonomy.

 2aws-region = us-east-1
 5num-nodes = 1
 8program = blastn
 9db = pdbnt
10queries = s3://elasticblast-test/queries/RFQT01.1.fsa_nt.gz
11results = ${YOUR_RESULTS_BUCKET}
12options = -outfmt 7 -taxids 1866885,1804623