How to run BLAST for quick similarity?

Install BLAST Software

• Visit the NCBI BLAST+ download page on the official NCBI website and download the appropriate version (Windows, Mac, or Linux) for your operating system.

 

• Follow the installation instructions specific to your operating system. For Windows, this might include running an executable installer. For Mac and Linux, decompress the files and add the directory to your system's PATH variable.

Prepare Your Query Sequence

• Ensure that your sequence is in FASTA format. A valid FASTA sequence starts with a header line beginning with a '>' sign, followed by lines of sequence data.

 

• If converting from another format, use software like BioEdit or EMBOSS to reformat the sequence into FASTA format.

Choose the BLAST Program

• Select the appropriate BLAST program based on your needs: BLASTn for nucleotide sequences, BLASTp for protein sequences, BLASTx for translating nucleotide sequences against a protein database, etc.

 

• Consider the type of sequences and the database you want to search against when making your selection.

Download or Choose a Database

• Decide if you are using a local database or the remote NCBI database. If using a local database, make sure it is downloaded and formatted properly with tools like `makeblastdb`.

 

• For quick local search, databases like 'nt' for nucleotides or 'nr' for proteins are commonly used.

Run the BLAST Search

• Open your command-line interface (CLI) or terminal.

 

• Use the appropriate BLAST command. For example: `blastn -query query.fasta -db nt -out results.txt`.

 

• Important command-line options include `-query` for the input file, `-db` for the database, `-out` for the output file, and `-evalue` for setting a threshold E-value (default is 10).

 

• Additional parameters can refine your search, such as `-max_target_seqs` for limiting the number of target sequences, or `-outfmt` for choosing the output format.

Analyze the Results

• Open the output file specified in the `-out` flag of your BLAST command to explore the results.

 

• Check for alignments and similarity scores to understand the sequence similarity. Focus on high-scoring pairs (HSPs) and E-values to determine the significance of matches.

 

• For detailed insight, consider visualizing results with tools like BLAST Graphic Summary or integrating results into bioinformatics software for further analysis.