You need to get the standalone BLAST tool installed on your desktop before you could do command-line BLAST. This tutorial is for Windows systems.
1.Download the standalone Blast from here
1a.Download database from here..ftp://ftp.ncbi.nlm.nih.gov/blast/db/.
it is painfully slow.
This is a mirror site of the genbank genome and this is a little faster.
2.Now create a folder in a non-C drive and extract the contents there. You should now have bin, data, db and doc.
Bin has the .exe files for the blast and data has the scoring matrices and db has the database(not yet though). Doc has documents for the individual programs in Bin.
3.Now let us assume that you installed the files in the E: drive. So you need to direct Windows to the E: drive everytime the software is run, whch means you need to create some sort of a signpost.
3a.Launch a notepad and copy paste the section below.
Substitute E: with whatever drive you are using. Name the file as “ncbi.ini” using “save as” option. Make sure to have the quotes for “ncbi.ini”, otherwise Windows stores it as a .txt file.
Now move this .ini file to C:\Windows folder.
You are ready to go now…