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BLAST is a Registered Trademark of the National Library of Medicine
Bookshelf ID: NBK569840
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BLAST® Command Line Applications User Manual [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-.
Starting with BLASTDB version 5, blastdbcmd has two additional parameters (-taxids and -taxidlists) to efficiently retrieve sequences by taxid.
# Retrieves all human entries;
# %a prints the accession, %T prints the taxid, %S prints the scientific name
$ blastdbcmd -db nr -taxids 9606 -outfmt “%a %T %S” -target_only
Note: -target_only is used to ensure that only accessions for the human entries are present. Otherwise, it will present all accessions on any sequence with at least one human sequence. This is important since nr is a non-redundant database.