BLAST from terminal against NCBI database using Perl

Using a Perl script you can BLAST your FASTA sequence file against the NCBI database directly from your terminal.

The script is provided by the NCBI and you can download it here: ftp://ftp.ncbi.nlm.nih.gov/blast/documents/web_blast.pl

The simple usage is:

$ perl web_blast.pl <program> <database> <query>

program: megablast, blastn, blastp, rpsblast, blastx, tblastn, tblastx
database: nt (Nucleotide), nr (non-redundant nucleotide), cdd (Conserved Domain Database), more…
query: your FASTA sequence file

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2 Responses to BLAST from terminal against NCBI database using Perl

  1. David Streid says:

    If we were using blastn to align two sequences, query.fasta to subject.fasta, is specifying the database necessary? Could we just use “perl web_blast.pl blastn query.fasta subject.fasta”?

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