I'm trying to run BLASTp against the nr proteins database, but I would like to restrict my alignments to some given levels of taxonomy. I've been reading that with the new v5 formats of BLAST databases this can be done by using the arguments -taxid or -taxidlist, but all the examples I've seen are for BLASTn and this argument doesn't seem to be available for BLASTp. Since I can do this search on my browser, is there any way to limit my search by taxonomy in BLASTp using the terminal?
Thank you in advance.
As long as you are doing the search locally you can use the options @shelkmike mentions. I don't think you can use them for remote blast searches at NCBI using a local terminal.