Install BLAST on Windows

BLAST, the Basic Local Alignment Search Tool, one of the most widely used bioinformatics programs, provides a way for researchers to quickly search huge databases of protein and amino acid sequences. 

BLAST enables access to the wealth of genetic information hosted at the National Center for Biotechnology Information (NCBI), part of the U.S. National Institutes of Health (NIH).  

In addition to searching at the publicly available website, researchers can download the BLAST program and run it locally.  Many free, publicly available databases can be downloaded, or researchers can create custom databases for searching and comparing local alignments. 

The following steps may be helpful for installing the BLAST program locally on a Windows machine. 

1. Open a browser window and go to
2. In some browsers, you may not be able to see the full name. Click on the first file that ends in w, or right-click and select download. This should be  ncbi-blast-2.2.29+-win32.exe, the 32-bit version, which should work on most Windows systems. If you know you have a 64-bit machine, you can select the one below it.

3. Save it to your Downloads folder. In Chrome, the file shows up in the lower corner of the browser window.

4. Click on the file in Chrome to run it, or use the Windows File Explorer to go to your downloads folder and click (or double-click) on the file to run it.

5. If you see the “Windows protected your PC” notice, click on “More info”.

6. Then click “Run Anyway”.

7. The install box will open. Click “I Agree”.

8. Click “Install”.

9.  When installation is completed, click “Close”.

10.  Hold down the Windows key and hit X (Win-X) to call up the Windows menu. Hit E or select the “File Explorer” menu option, and go to:

11. You should see blastp, blastn, and other executable files. These are the programs that can be run “from the command line”.

12. Back up to the following folder, so you can see the bin folder:  

13. Right-click on the bin folder and click “Open Command Window as Administrator”.

14. If you don’t have that option, hold down the Windows key and hit X (Win-X) and then click “Command Prompt Admin”.

15.  If the path shown is not the desired bin folder, type the two commands below. Hit the Enter key after each command to execute it. 

$ cd\
$ cd Program Files\NCBI\blast-2.2.29+\bin

16. Type  dir and hit the Enter key to see the BLAST executable files. dir is short for “show directory contents”.

17. From the bin folder, type the following command to make a new directory called “db” under the bin folder. This can be used to hold database and query files when working. mkdir is short for “make directory”. 

18. More instructions on running BLAST are available in the Blast User Manual available at:

Additional Genomics and Bioinformatics Links: