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How to run BLAST with custom organism DBs?

Learn to run BLAST with custom organism databases: setting up your environment, preparing and formatting databases, running searches, and reviewing results effectively.

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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.
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  • 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.

 

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