Body: <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-20T14:34:31.293Z
Comments.Text: https://bioinformatics.stackexchange.com/questions/7384/taxon-exclude-list-for-searching-local-blast-database-using-blastn
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-22T11:35:54.390Z
Comments.Text: 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 https://www.ncbi.nlm.nih.gov/guide/all/ for more detail.
Comments.UserDisplayName: Stuber
Tags: <blastn><nt>
Title: exclude uncultured and environmental samples from NT databases
ThreadText: # exclude uncultured and environmental samples from NT databases
  
  (Asked by: username_0 on 2019-12-20)
  
  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?
  
  **Tags:** blastn, nt
  
  > **Comments:**
  > **username_1**: https://bioinformatics.stackexchange.com/questions/7384/taxon-exclude-list-for-searching-local-blast-database-using-blastn  
  > **username_2**: 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 https://www.ncbi.nlm.nih.gov/guide/all/ for more detail.  
  
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  ## 0 answers
  
  