BLAST help

[horvathdp]

Hi all. I downloaded blast, and can make it work fine when I blast one data set against another (after formatting them) , but I can't seem to get the program to do a blast against the nr database that I downloaded and unpacked. My command lines is: blastn -query C:\Users\horvathd\Desktop\DREB.fa -db nr -out C:\Users\horvathd\Desktop\Dreb_vs_nr.txt -evalue 1e-5 -num_alignments 20 -outfmt 0 -num_descriptions 20

I get the following error

BLAST Database error: No alias or index file found for nucleotide database [nr]
in search path [C:\Program Files\NCBI\blast-2.2.24+\bin;;]

I unpacked the nr files in the "bin" folder. I can blast the DREB.fa file against other databases I have created with no problem. Any idea what I am doing wrong?

[cliffbeall]

Ok here is what I think might be the problem: What NCBI calls nr on their ftp site is a protein database. They call their non-redundant nucleotide database nt on the ftp site. The command line BLAST would use those names, so you would blastn against nt and blastx against nr. The BLAST web interface calls the nucleotide db nr/nt. It is confusing and has tripped me up before.