BLAST ON UNIX/LINUX TERMINAL

 If you work with DNA, RNA, or proteins, BLAST is one of those tools you end up treating like an old friend. Basic Local Alignment Search Tool (BLAST) is a high-speed algorithm that compares a query sequence against massive biological databases to find regions of similarity. In everyday scientific life, BLAST helps you to Identify unknown sequences, predict gene or protein function, detect evolutionary relationships, annotate genomes, Spot antimicrobial resistance genes and Validate cloning and PCR results among others.

Think of BLAST as the Google Search of molecular biology except it scans nucleotides and amino acids instead of web pages.


How to Install Standalone BLAST on Unix/Linux

1. Download the BLAST+ Executables

Head to NCBI’s FTP server and grab the latest BLAST+ release:

wget https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-*.x64-linux.tar.gz

*Requirement x64 bits system.

 

2. Extract the Package

tar -xvzf ncbi-blast-*.tar.gz

You should see a folder called ncbi-blast-2.15.0+.

 

3. Add BLAST to Your PATH

echo 'export PATH=$PATH:/path/to/ncbi-blast-2.15.0+/bin' >> ~/.bashrc && source ~/.bashrc

 

4. Verify Installation

blastn -version

If you see a version number, congratulations!!! You are ready to have a BLAST!

 

TIME TO BLAST OFF!!!

Step 1: Prepare or Download a Database

Your FASTA file with the collection of your sequence of interest to serve as a vault. It isn’t just a file, it’s the start of your personal BLAST database.

makeblastdb -in my_sequences.fasta -dbtype nucl -out mydb

For proteins:

makeblastdb -in proteins.fasta -dbtype prot -out myprotein_db

 

Step 2: Run BLAST with a Query Sequence

BLASTn (DNA vs DNA)

blastn -query query.fasta -db mydb -out nucleotide_hits.txt

 

BLASTp (Protein vs Protein)

blastp -query protein.fasta -db myprotein_db -out protein_hits.txt

 

BLASTx (DNA translated → Protein database)

blastx -query transcript.fasta -db nr -out transcript_hits.txt

 

Step 3: Explore the Results

BLAST results come as:

  • Tabular (outfmt 6): Perfect for pipelines and downstream analysis
  • Pairwise alignment: More readable for interpretation

 

I hope you had a BLAST!

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