Command blast excluding species

Question

[Adrian Pelin]

Hello,

When using NCBI's interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?

I need to exclude one species from my search. I see this can somehow be done with a GI list, but the example they give is not very understandable.

Adrian

Answer 1

[5heikki]

Use NCBI's taxonomy browser and link from there to genbank GI list of all nucleotides or proteins. Download that and use it in the command line blast, for example from here to here, then "send to" -> "file" -> "GI list"

[Adrian Pelin]

Excellent strategy. Although I must say, I am wondering why they do not simply the same approach available in the online interface, where you can simply restrict your analysis to a taxid or exclude it from your analysis.