BLAST UNIX Tutorial

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This is a quick outline of how to make a local database and run BLAST on sequence files against these databases or online ones like nr.

BLAST+

The command line (UNIX or Windows) version of BLAST is named BLAST+. You can download it from [1]. The user manual for BLAST+ is [2] and contains instructions on installation of the command line tools. This covers all of the functionality of blast+. Here, only a sunset of features and basic usage will be covered.

Basic use

Blast+ will do all the regular searches: blastn, blastp, blastx, tblastx, tblastn, and less used but still relevant searches psiblast, rpsblast, and rpstblastn.
Each tool is run by typing the search name into your command line followed by certain options (called flags).
For example if I wanted to run blastx on a file called seqs.fasta, output the result to a file output.blast.txt and keep all the default settings I would navigate to the folder where seqs.fasta is stored and type

blastx -in seqs.fasta -out output.blast.txt

This is considering that blast+ was placed into my path (which should have occurred during installation. If not you would type the full path of the location of the blast bin folder before blastx)

Changing parameters

Many sections of the blast search can be modified such as the e-value cut-off, output format, number of hits to retain and much more. A full list of these options is covered in the manual and an out