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:
BioContainers: https://biocontainers.pro/tools/blast
Home page: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMDWeb&PAGE_TYPEBlastHome

Versions

  • 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

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=blast
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load blast/XXXX ### you can run *module avail blast* to check all available versions

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