Access NCBI blast through command line without downloading entire nr database?

Question

[allison.sharrar]

Is there a way to run a blast against NCBI's nr database through the command line without downloading the entire database?

Answer 1

[GenoMax]

Yes there is. Use -remote option when you use the command line blast locally. This will allow you to search at NCBI. Not meant to be used with hundreds of queries but for a small number of well separated ones this will work fine. You will obviously need direct internet access for this to work.