Local/Standalone BLAST on Unix Platform


Setting up :

  1. Set a directory and name it “blast”.
  2. Download Unix binary of BLAST, uncompress and untar the file.
  3. Create a .ncbirc file and specify the path where the file has been stored e.g.



Formatting database :

  1. Check that .ncbirc file is in the directory where standalone BLAST is called from
  2. Format the database file with the following command line:

formatdb -i database.name -p F -o T (for nucleotide database)
formatdb -i database.name -p T -o T (for protein database)

This will create index files required by standalone BLAST to perform searches.
[-i = input, -p = protein, F if false, T if true, -o = output]


Performing BLAST by command line:

blastall -p blast_program -d database.name -i input.name -o output.name

blastall : calls for BLAST program
-p : calls for program name – blastp, blastn, blastx, tblastn or tblastx
-d : calls for database name
-i : calls for input name i.e. the set of queries to be searched against the database
-o : calls for output file


Other criteria to note for:

-e : expected value, default = 10.0
-v : number of database sequences to show one-line descriptions for, default = 500 (use 1 to give the best hit)
-b : number of database sequences to show alignments for, default = 250 (use 1 to give the best alignment)
-a : number of processor(s) to use for computation


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