How to specify organism taxa in biopythons remote blast cmd?

Question

[tim.ivanov.92]

I' doing tblastn with biopython via

from Bio.Blast import NCBIWWW
fasta_string = open("my_query.faa").read()
result_handle = NCBIWWW.qblast("tblastn", "refseq_genomes", fasta_string )

and i want to limit my search only to one taxa - arthropods (taxid:6656)

In web blast it is easily done, but i can't seem to find the right option here.

Answer 1

[Sej Modha]

Hi there,

I think entrez_query option should do the job e.g. entrez_query='txid6656[ORGN]' http://biopython.org/DIST/docs/api/Bio.Blast.NCBIWWW-module.html

entrez_query Entrez query to limit Blast search

[tim.ivanov.92]

Thank you - that does it!