How to set up a local Blast database

Get to directory where you put Blast files
Type in the following:
makeblastdb -in file -out name -dbtype prot
-hash_index
(for a database of proteins)
OR
makeblastdb -in file -out name -dbtype nucl
-hash_index
(for a database of DNA or RNA)


What it means:

• makeblastdb invokes the Blast accessory program to create the database
• -in tells the program that the path that follows leads to the input file.
• -out tells the program that the characters that follow should be used as the name of the database (you can name it anything you want, so long as you use 8 or fewer legal characters).
• -dbtype prot Tells the program "the file does consist of protein sequences".
  -dbtype nucl tells the program "the file consists of nucleotide sequences"
• -hash_index tells the program "you should make an index of the identification numbers for the sequences" Frankly, I don't know what good the index does, but it's cheap.

WARNING #1: Upper/Lower case matters for the commands following -!

WARNING #2: Windows XP and NT users may experience trouble cutting and pasting the command line makeblastdb. Evidently the system does something strange to the hyphens. Type the command in instead.

From:http://www.vcu.edu/csbc/bbsi/inst/archives/bioinf/SetupLocalBlast.html