Types of BLAST, applications, Algorithm & interpretation of results

Installation of Standalone BLAST on Windows PC

Reasons for installing the standalone BLAST+ package

You can also download the BLAST package to perform sequence alignments on your computer, including using your custom datasets. A few example scenarios for setting up the BLAST+ package locally are:

1. Large batches of searches and searches that are computationally intensive, such as searches involving
   dynamic translation of nucleotide sequences (blastx, tblastn, or tblastx)
2. Target datasets that are not available at NCBI
3. BLAST only serves as an intermediate step within a complex workflow that needs to be automated
4. Searches requiring customization that cannot be satisfied by the BLAST web service.

Download BLAST+

• Visit the NCBI FTP server: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
• Determine your Windows system architecture (32-bit or 64-bit) by following these steps:
  • Press the Windows key + R to open the Run dialog.
  • Type “dxdiag” and press Enter.
  • In the DirectX Diagnostic Tool window, look for the “Operating System” section. It will display whether your system is running a 32-bit or 64-bit version of Windows.
• Download the appropriate BLAST+ installer for your system architecture (e.g., ncbi-blast-2.x.x+-x64-win64.exe for 64-bit Windows).

Install BLAST+

1. Locate the downloaded BLAST+ installer file and double-click on it to run the installation wizard.
2. When prompted, click “Next” to proceed with the installation.
3. Read and accept the license agreement by selecting “I accept the agreement” and clicking “Next.”
4. Choose the installation folder or accept the default location by clicking “Next.”
5. Select the components you want to install. It’s recommended to install all components unless you have specific requirements.
6. Click “Next” to start the installation process.
7. Wait for the installation to complete, and then click “Finish” to exit the installer.

Add BLAST+ to the System PATH

1. Right-click on the “Start” button and select “System.”
2. Click on “Advanced system settings” on the left-hand side.
3. In the “System Properties” window, click on the “Environment Variables” button at the bottom.
4. In the “Environment Variables” window, under the “System Variables” section, scroll down and find the “Path” variable, then click “Edit.”
5. Click “New” and paste the path to the BLAST+ bin directory (e.g., C:\ncbi-blast-2.x.x+\bin).
6. Click “OK” to save the changes and close all windows.

Verify Installation

• Open a new Command Prompt (cmd.exe) window.
• Type the following command and press Enter:
  blastn -version
• If the installation was successful, you should see the BLAST+ version information displayed in the Command Prompt window.

Set up BLAST Databases (Optional)

• BLAST requires sequence databases to perform searches. You can download pre-formatted databases from the NCBI FTP server or format your databases using the makeblastdb tool.
• To format your database, follow these steps:
  • Obtain your sequence data in FASTA format.
  • Open a Command Prompt window and navigate to the BLAST+ bin directory (e.g., cd C:\ncbi-blast-2.x.x+\bin).
  • Run the makeblastdb command with the appropriate options for your sequence type (nucleotide or protein):
    makeblastdb -in your_sequences.fasta -dbtype <type> -out your_database_name
    Replace <type> with nucl for nucleotide sequences or prot for protein sequences.

Running BLAST Searches

• Once you have your sequence databases set up, you can run BLAST searches using the appropriate BLAST+ program:
  • blastn for nucleotide sequences against a nucleotide database
  • blastp for protein sequences against a protein database
  • blastx for translated nucleotide sequences against a protein database
  • tblastn for protein sequences against a translated nucleotide database
  • tblastx for translated nucleotide sequences against translated nucleotide databases
• Open a Command Prompt window and navigate to the directory containing your query sequences.
• Run the desired BLAST program with the appropriate options and arguments. For example:
  blastn -query your_query.fasta -db path/to/database -out results.txt
  This command runs a nucleotide BLAST search using your_query.fasta as the query sequence against the specified database, and saves the results in results.txt.

Additional Resources

1. For more detailed information, refer to the BLAST+ documentation available on the NCBI website: https://www.ncbi.nlm.nih.gov/books/NBK279690/
2. The NCBI also provides online BLAST tutorials and webinars: https://www.ncbi.nlm.nih.gov/staff/tao/tools/bat/
3. Links to different help documents are online at: https://blast.ncbi.nlm.nih.gov/Blast.cgiCMD=Web&PAGE_TYPE=BlastDocs
4. More information on standalone BLAST is available from the BLAST user manual: https://www.ncbi.nlm.nih.gov/books/NBK1762/
5. Comments, questions, bug reports, and assistance requests to: blast-help@ncbi.nlm.nih.gov

By following these detailed steps, you should be able to successfully install and set up the standalone BLAST+ on your Windows PC, format sequence databases, and run various BLAST searches as needed.

Reference

Tao, T. (2020, August 31). Standalone BLAST setup for Windows PC. BLAST® Help – NCBI Bookshelf. https://www.ncbi.nlm.nih.gov/books/NBK52637/