I am running a local blast server. I can format and blast my own databases. However, I am unsure of how to setup the "Nucleotide collection nr/nt" database from this NCBI Blast URL.
Can I just download a preformatted db and use the update script? Which database is it? Is it just both the nr and nt databases? Isn't blastn used for the nt database and blastp used for the nr database? Can I blast them both at the same time? If so how?
Also, downloading nr downloads two files nr.01.tar.gz and nr.00.tar.gz. Is this right? How can I setup to blast just "nr" rather than "nr.00 nr.01"?
I have been using the following commands:
blastp -word_size 7 -evalue 10 -query test.fasta -db "nr.00 nr.01"
and blastn -word_size 11 -evalue 10 -query test.fasta -db nt.00
Thank you for your help!