How to run BLAST with custom organism DBs?

Prepare Your Environment

• Ensure you have the BLAST+ suite installed on your system. You can download it from the NCBI website.

 

• Create a working directory where you will store your custom organism database and query files.

Prepare the Custom Database

• Gather your sequence data in FASTA format. This could be genomic, protein, or nucleotide sequences specific to your organism.

 

• Place your FASTA files into the working directory you've created.

Format the Custom Database

• Use the makeblastdb tool from the BLAST+ suite to convert your FASTA file into a BLAST database.

 

• Run the following command, replacing input.fasta with your FASTA file, and db\_name with your chosen database name:

  makeblastdb -in input.fasta -dbtype nucl -out db\_name

 

• Use the -dbtype option to specify whether your sequences are nucleotide (nucl) or protein (prot).

Prepare Your Query Sequence

• Ensure your query sequence is in FASTA format. This is the sequence you will BLAST against your custom database.

 

• Save this file in your working directory as well.

Run BLAST Search

• Use the blastn command for nucleotide queries or blastp for protein queries.

 

• Execute the following command, replacing query.fasta with your query file, db\_name with your database name, and output.txt with your desired output file:

  blastn -query query.fasta -db db\_name -out output.txt

 

• You can customize the BLAST command with additional options, such as -evalue for setting an E-value threshold or -outfmt for different output formats.

Review Results

• Once the BLAST search completes, examine the output file (output.txt) to review your BLAST results.

 

• Look for significant alignments, E-values, and other statistics relevant to your research objectives.