I presume that you have already downloaded and installed Blast (if not, then click here) and downloaded the FastA-formatted sequence file that will serve as the basis for the Blast database (if not, then do it).
Blasting the contigs against the genome of an organism proceeds in two stages. First, you need to let Blast analyze the genome sequence to create a database it can understand. Later you'll run Blast to compare each contig to that database.
|Get to a DOS window||The Blast you downloaded is a DOS-based program. You can get to DOS in one of several ways: (a) You may find shortcut if you click on Start and then on Programs, or (b) Click on Start and then Run. Type in Command or Cmd|
|Get to directory where you put Blast files||Type in something like CD \Blast|
|Type in the following:
makeblastdb -in file -out name -dbtype prot
(for a database of proteins)
makeblastdb -in file -out name -dbtype nucl
(for a database of DNA or RNA)
|What it means:
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.