Applications/Ncbi-blast

Application Details

• Description: NCBI-Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
• Version: 2.4.0 , 2.6.0
• Modules: ncbi-blast/2.4.0, ncbi-blast/2.6.0
• Licence: Open-source (BLAST is a registered trademark of the National Library of Medicine)

Usage Examples

Command Set

ncbi-blast provides the following commands:

• blast_formatter
• blastdb_aliastool
• blastdbcheck
• blastdbcmd
• blastn
• blastp
• blastx
• convert2blastmask
• deltablast
• dustmasker
• legacy_blast.pl
• makeblastdb
• makembindex
• makeprofiledb
• psiblast
• rpsblast
• rpstblastn
• segmasker
• tblastn
• tblastx
• update_blastdb.pl
• windowmasker

Interactive Session

[username@login01 ~]$ interactive
salloc: Granted job allocation 3619736
Job ID 3619736 connecting to c081, please wait...
c081.vc-main
[username@c081 ~]$ module add ncbi-blast/2.
ncbi-blast/2.11.0  ncbi-blast/2.12.0  ncbi-blast/2.4.0   ncbi-blast/2.6.0
[username@c081 ~]$ module add ncbi-blast/2.6.0
[username@c081 ~] blastp <user options>

Batch Script

#!/bin/bash

#SBATCH -J blast
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -o job-%j.out
#SBATCH -e job-%j.out
#SBATCH -p compute

# perfoms NR blast (blastx)
infile="$1"
outfile="$(basename "${infile%.*}").xml"
database="/swissprot/uniprot_sprot"

module purge
module load ncbi-blast/2.6.0

blastp \
 -query "${infile}" \
 -db "${database}" \
 -out "${outfile}".xml \
 -evalue 1e-5 \
 -num_threads 8 \
 -max_target_seqs 50 \
 -outfmt 5

Further Information

• https://blast.ncbi.nlm.nih.gov/Blast.cgi

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