Organism Search Setting in Blast+

Question

[kevluv93]

I've installed and downloaded blast+, utilizing the -remote function to BLAST my data against NCBI's database. I'm mostly happy with the outputs, but is it possible to use the "organism" function like on the online NCBI BLAST on the blast+ command line?

So if I wanted to use BLAST+ and only BLAST against NCBI's database of Drosophila, could I do that? How can I do that? I'd prefer not to download the library of Drosophila they have on NCBI onto a local database, I'm sure I'm not the only person who's ever done this before.

Thank you and have a great day!

[Kumar]

The following command may help

$blastn -remote -db nr -query <path> -entrez_query "Drosophila, [Organism]" -evalue 1e-30 -outfmt 6 -qcov_hsp_perc 100

Answer 1

[h.mon]

I believe something like -entrez_query='drosophila[organism]' is what you want.

[kevluv93]

I'll definitely do that. Right now it's late so I'm going to try it tomorrow. I'll let you know how it goes