Question: Organism Search Setting in Blast+
0
gravatar for kevluv93
3.8 years ago by
kevluv93150
United States
kevluv93150 wrote:

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!

blast sequence alignment • 1.1k views
ADD COMMENTlink modified 3.8 years ago by h.mon24k • written 3.8 years ago by kevluv93150
1

the following command may help

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

ADD REPLYlink written 3.8 years ago by Manoj30
2
gravatar for h.mon
3.8 years ago by
h.mon24k
Brazil
h.mon24k wrote:

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

ADD COMMENTlink written 3.8 years ago by h.mon24k

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

ADD REPLYlink written 3.8 years ago by kevluv93150
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