Step-by-Step Guide: Install Local BLAST in Ubuntu

Install Local BLAST in Ubuntu

Step 1: Update Your System

Before installing any software, ensure your system is up-to-date:

sudo apt update
sudo apt upgrade

Step 2: Install BLAST+ Using apt

The easiest way to install BLAST is through the Ubuntu package manager:

sudo apt install ncbi-blast+

Step 3: Verify Installation

Check if BLAST is installed correctly:

blastn -version

This should display the installed version of BLAST.

Step 4: Download and Install BLAST Manually (Optional)

If you prefer to install the latest version manually, follow these steps:

1. Download BLAST+ from NCBI:
   • Visit the BLAST+ download page.
   • Download the Linux version (e.g., ncbi-blast-2.14.0+-x64-linux.tar.gz).
2. Extract the Archive:
   bash

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   tar -xvzf ncbi-blast-2.14.0+-x64-linux.tar.gz

3. Move to a System Directory:
   bash

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   sudo mv ncbi-blast-2.14.0+ /usr/local/blast

4. Add BLAST to Your PATH:
   Edit your .bashrc or .zshrc file:
   bash

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   echo 'export PATH=/usr/local/blast/bin:$PATH' >> ~/.bashrc
   source ~/.bashrc

5. Verify Installation:
   bash

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   blastn -version

Step 5: Download and Prepare a BLAST Database

To use BLAST locally, you need a database. You can download pre-formatted databases from NCBI or create your own.

1. Download a Pre-Formatted Database:
   • Visit the NCBI BLAST Databases.
   • Download a database (e.g., nt for nucleotide sequences):
     bash

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     wget https://ftp.ncbi.nlm.nih.gov/blast/db/nt.00.tar.gz
     wget https://ftp.ncbi.nlm.nih.gov/blast/db/nt.01.tar.gz

2. Extract the Database:
   bash

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   tar -xvzf nt.00.tar.gz
   tar -xvzf nt.01.tar.gz

3. Place the Database in a Directory:
   bash

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   mkdir ~/blastdb
   mv nt* ~/blastdb

Step 6: Run a Local BLAST Search

Now you can run BLAST searches locally using your database.

1. Prepare a Query File:
   Create a FASTA file (e.g., query.fasta) with your sequence:
   bash

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   echo ">query_sequence" > query.fasta
   echo "ATGCGATCGATCGATCGATCGATCGATCGATCG" >> query.fasta

2. Run BLAST:
   Use the blastn command to search against the nt database:
   bash

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   blastn -query query.fasta -db ~/blastdb/nt -out results.txt

3. View Results:
   bash

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   cat results.txt

Step 7: System Requirements

• Minimum Requirements:
  • RAM: 4 GB (8 GB or more recommended for large databases).
  • Disk Space: At least 10 GB for databases (varies depending on the database size).
  • Processor: Multi-core processor for faster performance.
• For Large Databases:
  • Use a machine with 16+ GB RAM and SSD storage for better performance.

Recent Online Tools and Software

1. NCBI BLAST Web Interface: https://blast.ncbi.nlm.nih.gov
2. SequenceServer: A web-based BLAST interface for local use. https://sequenceserver.com
3. Galaxy: A platform for bioinformatics analysis, including BLAST. https://usegalaxy.org

Conclusion

By following these steps, you can install and configure a local BLAST setup on Ubuntu. This allows you to perform BLAST searches without relying on online tools, which is especially useful for large datasets or sensitive data.