I've created two custom databases using blastn from the command line in Ubuntu. Each database is a different genomic sequence of the same species. The output for these custom databases each contained 3 files, .nhr, .nin and .nsq. The NCBI BLAST help manual says the command for running blast is
blastn –db nt –query nt.fsa –out results.out
I've tried researching this and playing around with the above command by using the file names, locations, etc. that apply to the files I'm trying to blast, but I cannot figure out what the appropriate version of this command is for my task. Any tips? Thanks in advance. I'm an undergrad studying biology.