BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.


  • 2.11.0

  • 2.13.0


  • blastn

  • blastp

  • blastx

  • blast_formatter

  • amino-acid-composition

  • between-two-genes

  • blastdbcheck

  • blastdbcmd

  • blastdb_aliastool


  • deltablast

  • dustmasker

  • eaddress

  • eblast



  • makeblastdb

  • makembindex

  • makeprofiledb

  • psiblast

  • rpsblast

  • rpstblastn

  • run-ncbi-converter

  • segmasker

  • tblastn

  • tblastx


  • windowmasker


You can load the modules by:

module load biocontainers
module load blast

BLAST Databases

Local copies of the blast dabase can be found in the directory /depot/itap/datasets/blast/latest/. The environment varialbe BLASTDB was also set as /depot/itap/datasets/blast/latest/. If users want to use cdd_delta, env_nr, env_nt, nr, nt, pataa, patnt, pdbnt, refseq_protein, refseq_rna, swissprot, or tsa_nt databases, do not need to provide the database path. Instead, just use the format like this -db nr.

Example job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run BLAST on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 1
#SBATCH --job-name=blast
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers blast

blastp -query protein.fasta -db nr -out test_out -num_threads 4