BLAST

Introduction

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.

For more information, please check its website: https://biocontainers.pro/tools/blast and its home page: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome.

Versions

  • 2.11.0

  • 2.13.0

Commands

  • blastn

  • blastp

  • blastx

  • blast_formatter

  • amino-acid-composition

  • between-two-genes

  • blastdbcheck

  • blastdbcmd

  • blastdb_aliastool

  • cleanup-blastdb-volumes.py

  • deltablast

  • dustmasker

  • eaddress

  • eblast

  • get_species_taxids.sh

  • legacy_blast.pl

  • makeblastdb

  • makembindex

  • makeprofiledb

  • psiblast

  • rpsblast

  • rpstblastn

  • run-ncbi-converter

  • segmasker

  • tblastn

  • tblastx

  • update_blastdb.pl

  • windowmasker

Module

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

Warning

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:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=blast
#SBATCH --mail-type=FAIL,BEGIN,END
#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