Wednesday, 2 May 2012

Install standalone blast for windows

BLAST allows you to compare your sequence against a database of sequences and informs you if your sequence matches any of the sequences in the database.

The ncbi-blast-#.#.#+-win32.exe is compatible with PCs running Windows XP, 32-bit Vista or Windows 7.
ncbi-blast-#.#.#+-win64.exe is compatible with PCs running  Windows XP 2003, 64-bit Vista or Windows7. "#.#.#" denotes the current version number of the package.

Installation steps

1. Download blast((ncbi-blast-2.2.26+-win32.exe) from

2. Double click the ncbi-blast-2.2.26+-win32.exe . Accept the license agreement.Then the installer will     prompt for an installation directory. The default installation directory is "C:\blast-2.2.25+".
(you can choose any other destination folder)

3. click the install button. It will install blast in C:\blast-2.2.25+

4. Next step is to configure the environment variable.
   Go to Start -> My Computer
   Right click My Computer and click Properties.
   System Properties pop up will open.
   In the popup, click on the Advanced tab
   Click the "Environment Variables" button
   Click the "New" button under the "User variable for ..." panel.
       variable name : Path
       variable value: C:\blast-2.2.25+\bin
click ok button.

5. Create the Blast database

The blast+ installer automatically creates a BLASTDB environment variable, which points to the "C:\blast-2.2.25+\" directory. For more effective database management, a "db" subdirectory should be created under the "C:\blast-2.2.25+\".
The value of BLASTDB environment variable must be modified to "C:\blast-2.2.3+\db\".
Pre-formatted NCBI BLAST databases is available as compressed archives from NCBI ftp site.You can download the database and put in the db folder. The second option is you can create a custom database. Databases can be prepared from custom FASTA sequences locally using the makeblastdb utility.

To create a custom BLAST database, you need a simple FASTA file say nuclic.fasta. Put all your FASTA sequence in it. Put the nuclic.fasta file in C:\blast-2.2.25+\db folder. The custom sequence's fasta file (nuclic.fasta)is then converted into BLAST database by a tool called makeblastdb.(you can see makeblastdb.exe file in C:\blast-2.2.25+\bin folder)

To create blast database file
Open the command promt.
The below image show the execution of makeblastdb command.

the command is
makeblastdb -in db/nuclic.fasta -dbtype nucl -out db/nuclic

It will create 3 files nuclic.nhr, nuclic.nin, nuclic.nsq in  C:\blast-2.2.25+\db folder
.nsq, .nhr, and .nin files are blastn database files.

6. Create  test.txt file which contains the FASTA sequence to be compared.

This file is used as an input query in a test blastn search with the following command line:

blastn -query db/test.txt -db db/nuclic -out db/output.txt

which performs the following tasks:
    1. calling blastn to run a nucleotide query vs nucleotide database search
    2. using sequence contained in test.txt file as input query
    3. searching against nuclic database
    4. saving the result in output.txt
The below image show the execution of blastn command.

A new file output.txt is created in C:\blast-2.2.25+\db folder.


  1. very helpful tutorial.....Can you please give more examples of what can be done in standalone BLAST....

    1. The main advantage of Standalone blast is you can create your own BLAST databases. you can also integrate Blast in your web application using standalone blast. It performs all the functions of Blast.

  2. Is there any command to know the default parameter of standalone blast?