I'm working with a system that does local BLAST searches using some preconfigured BLAST databases. From what I see, these were updated within the last year, but I cannot find any current databases available that have those same names. One specific set is a non-redundant set of human protein or nucleotide sequences. The databases are named human_nr and human_nt (with various extensions as per the BLAST db format). There are others names up_sp_human (Uniprot-Swissprot human?) and up_tbl_human (Uniprot-Tremble human?), but a cannot find any similar databases on the NCBI site or other sites.

Where else should I look for such preconfigured databases?


1 Answer 1


I don't think there is a human_nr or human_nt database for NCBI.

An equivalent database is accessible via the standard nr/nt database and simply restrict the organism parameter to human or to taxa id 9606 . This essentially will do the same thing.

Or maybe this sort of thing?,

blastdbcmd -db nr -entry all -outfmt "%g %T" | awk ' { if ($2 == 9606) { print $1 } } ' > human_flat-list.db
  • 1
    $\begingroup$ This is super helpful! I'm guessing these were custom prepared similar to what you describe. Thank you! $\endgroup$
    – KirkD-CO
    May 12, 2023 at 14:23
  • $\begingroup$ Thanks for your feedback @KirkD-CO $\endgroup$
    – M__
    May 12, 2023 at 14:28

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