I'm using blast locally against NT databases and I'm excluding the uncultured and environmental samples by the taxonomy ID. Is there another way to exclude them entirely, without using the taxonomy ID?

  • $\begingroup$ bioinformatics.stackexchange.com/questions/7384/… $\endgroup$ Dec 20 '19 at 14:34
  • $\begingroup$ If trying to gain database quality by excluding uncultured and environmental, RefSeq may be helpful. Database can be downloaded locally. update_blastdb.pl --showall shows pre-formatted databases (refseq_genomic). See link, "Reference Sequence (RefSeq)" at ncbi.nlm.nih.gov/guide/all for more detail. $\endgroup$
    – Stuber
    Dec 22 '19 at 11:35

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