BLAST+ Basic Local Alignment Search Tool is a sequence homology search tool. Given a probe sequence (nucleotide or protein), BLAST compares it to a sequence database and picks out sequences with significant similarity to the probe sequence.

Below is a list of prerequisites for using BLAST+:

• GCC Compiler

To load BLAST+ type the following:

$ module load gcc blast+

This will set the BLASTDB environment variable to /share/apps/blast-2.2.25+/db

If your databases are located elsewhere you will need to set the BLASTDB variable to point to that location.

A “.ncbirc” file under the home directory can be created to configure the BLASTDB variable.

[BLAST] BLASTDB=/home/path/to/blast/db Upon start, BLAST will read this file to get the path information it needs during BLAST searches.

Search Commands

• blastn search hits for a nucleotide sequence from nucleotide database
• blastp search hits for a protein sequence from protein database
• blastx search hits for a nucleotide sequence from protein database
• psiblast do iterative search for a protein sequence from protein database
• rpsblast search hits for a protein sequence from protein profile database
• rpstblastn search hits for a nucleotide sequence from protein profile database
• tblastn search hits for a protein sequence from nucleotide database
• tblastx search hits for a nucleotide sequence from nucleotide database by using the protein translations of both query and database sequences.

Other blast commands

• blastdbcmd retrieve a sequence or a set of sequences form BLAST databases
• makeblastdb create a new BLAST database
• blast_formatter reformat a BLAST archive formatted BLAST result file

BLAST Manual