Limiting a Search by taxonomy

In order to limit a BLAST search by taxonomy, one needs to provide the NCBI taxonomy ID(s) (taxid) for given organism(s). A taxid is simply a number that specifies a node in the taxonomic tree. For example, 9606 is the taxid for human, 9989 is the taxid for rodentia, and 2 is the taxid for all bacteria. Taxids are preferable to organism names as the latter can be ambiguous. For instance, bacteria is both a genus of insects as well as a superkingdom.

Additionally, one may use the -negative_taxids and -negative_taxidlist options to exclude sequences by taxid.

$ blastn –db nt –query QUERY –taxids 9606 –outfmt 7 –out OUTPUT.tab