Standalone BLAST with Ruby (windows)

Updated article

BLAST is one of the most widely used search algorithms in molecular biology. So lets see how you can run and retrieve blast results via a simple Ruby script .I will assume you already have ruby 1.8.5 and above installed in your windows box and a standalone blast.exe which you can download from the NCBI’s ftp site here . The latest windows binaries as of this writing is 2.2.17. Create a new folder in C and call it NCBI_Blast. Paste the downloaded blast program in this folder. Double click the blast program and it will create a bin, doc and data folders inside your your NCBI_Blast folder. If this is your first time to install blast in your machine. You will need to do a little configuration. Follow these instructions for setting up blast .
#create a query sequence
#create a temporary file
require 'tempfile'"seqfile")
#get the name of the temporary file
#append the contents your sequence to this temporary file
temp.puts "#{myseq}"
#since we have a protein query sequence, we will run a blastp. Please note that you will need to have a valid #database to query against. use the formatdb command to create your database before executing the lines #below.
@program = 'blastp'
#path to blast
@database = 'c:/path_to_databasefile'
#name of your query file
@input= name
#your blast output file
#assume your blast is in a folder called NCBI_Blast, execute
system( "c:/NCBI_Blast/bin/blastall.exe -p #{@program} -d #{@database} -i #{@input} -o #{@output}")
#To capture the output in a variable execute this command instead.
#note that we have omitted the blast -o parameter
result=%x(c:/NCBI_Blast/bin/blastall.exe -p #{@program} -d #{@database} -i #{@input} )
#remember to delete the temporary file!


  1. jan.

    You can also use bioruby to run BLAST searches against local databases. Here’s a sample script:

    require 'bio'

    factory = Bio::Blast.local('blastn', '/path/to/BLAST/database')
    ff =, 'input_file.fa')
    ff.each do |entry|
    $stderr.puts "Searching..." + entry.definition
    report = factory.query(entry)
    report.each do |hit|
    hit.each do |hsp|
    puts hsp.query_from

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