How to set up a local Blast database

I presume that you have already downloaded and installed Blast (if not, then click here) and downloaded the contigs and the genomic sequence from either S. pneumoniae or S. mutans (if not, then click here).

Blasting the contigs against the genome of an organism proceeds in two stagaes. 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.

Action
Explanation and notes
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:
formatdb -ifile -nname -pF -oT		 What it means:
  • formatdb invokes the Blast accessory program to create the database
  • -i tells the program that the path that follows leads to the input file.
  • -n 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).
  • -pF tells the program "False, the file does not consist of protein sequences" It contains nucleotides. (-pT would have been appropriate for protein sequences)
  • -oT tells the program "True, 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 formatdb. Evidently the system does something strange to the hyphens. Type the command in instead.