Software: BLAST (Basic Local Alignment Search Tool)
Description
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.
Available Versions
Unspecified: | 2.11.0 2.13.0 |
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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.
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
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