Question: Filter command-line BLAST results by organism
0
gravatar for jdromano2
3.8 years ago by
jdromano210
Burlington, VT, USA
jdromano210 wrote:

In legacy blast (blastall) it was easy to do a remote BLAST query from the command line that only returned hits for a single organism:

blastall -u "[Arabidopsis thaliana[organism]" -p blastp -d nr -i my_protein_input.fas -o my_protein_input_vs_nr_Athaliana.blastout.txt

However, this seems to have been removed with the release of BLAST+. Aside from filtering hits after they are returned, is it possible to perform a query on the 'nr' database that only returns hits for a single specified taxon?

 
blast taxonomy alignment genome • 2.6k views
ADD COMMENTlink modified 3.6 years ago by agoel10 • written 3.8 years ago by jdromano210
1

I think you just add the -remote flag and use -entrez_query instead
 

ADD REPLYlink written 3.8 years ago by Chris S.290

how can use more than one species in the remote search.

Thanks

ADD REPLYlink written 3.1 years ago by Manoj20
1
gravatar for agoel
3.6 years ago by
agoel10
Australia
agoel10 wrote:

Im having a similar problem. It seems the best option is to create your own database. Make a blast_db with the fasta file for your organism if you have it, otherwise you have to do something like this:

  1. Download the prebuilt nr database (ncbi?).
  2. Search the Entrez Protein database with query: "txid7742[ORGN]"
  3. Select "Send to File" and choose format "GI list"
  4. Use the list of GIs from the previous step with the blastdb_aliastool to build an aliased blastdb of just your organism (takes several seconds), eg:

    blastdb_aliastool -gilist vertebrates.gi_list.txt -db nr -out nr_vertebrates -title nr_vertebrates

  5. Search against your new (aliased) database:

    blastx -query query.fa -db nr_vertebrates

( from this thread: Vertebrate Subset Nr Database? Build My Own? )

ADD COMMENTlink modified 3 months ago by h.mon16k • written 3.6 years ago by agoel10
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