Difference between revisions of "Applications/Ncbi-blast"

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* windowmasker
 
* windowmasker
  
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===Interactive Session===
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<pre style="background-color: #000; color: white; font-family: monospace, sans-serif;">
 +
 +
[username@login01 ~]$ interactive
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salloc: Granted job allocation 3619736
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Job ID 3619736 connecting to c081, please wait...
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c081.vc-main
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[username@c081 ~]$ module add ncbi-blast/2.
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ncbi-blast/2.11.0  ncbi-blast/2.12.0  ncbi-blast/2.4.0  ncbi-blast/2.6.0
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[username@c081 ~]$ module add ncbi-blast/2.6.0
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[username@c081 ~] blastp <user options>
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</pre>
  
 
===Batch Script===
 
===Batch Script===
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module purge
 
module purge
module load ncbi-blast
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module load ncbi-blast/2.6.0
  
 
blastp \
 
blastp \

Latest revision as of 12:11, 17 November 2022

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





Modules | Main Page | Further Topics