Revision as of 13:29, 5 April 2017

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
• Modules: ncbi-blast/2.4.0
• 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

SLURM Script

#!/bin/bash

fasta=/home/user1/maker.all.proteins.fasta
seqs_per_file=300
files_per_dir=100
BLAST_DB=/home/user1/database/nr_metazoa
prefix=Tcancriformis_maker2
threads_per_job=28
e=1e-5
cul=10
n_seqs=50
fmt=5 #5=xml
basedir=$(pwd)
partition_script=/home/user1/ectools/partition.py

###########

echo -e "\nsplitting up files\n"
#cat $fasta | sed 's/ .*//g' > $genome.fasta
python $partition_script $seqs_per_file $files_per_dir $fasta

count=$(ls -1 | grep -E "^[0-9]{4}" |wc -l)
for i in $(seq $count -1 1)
do
        current=$(printf "%04d" $i)
        echo -e "processing directory $current\n"
        cd $current

        for p in $(ls -1 | grep -E "p[0-9]{4}$" | sort -nr)
        do

                echo -e "#!/bin/bash
#SBATCH -J b-$current-$p-$prefix
#SBATCH -N 1
#SBATCH --ntasks-per-node $threads_per_job
#SBATCH -o job-%j.out
#SBATCH -e job-%j.out
#SBATCH -p compute

#LOAD MODULE
module load ncbi-blast/2.4.0
#
date
cd $basedir/$current

echo -e \"\\\nNumber of scaffolds to process:\\\t\$(cat $basedir/$current/${p} | grep \">\" | wc -l)\"
echo -e \"\\\nTotal length of scaffolds:\\\t\$(cat $basedir/$current/${p} | grep \">\" -v | perl -ne 'chomp; print \"\$_\"' | wc -m)\\\n\"

blastp -query ${p} -db $BLAST_DB -outfmt $fmt -max_target_seqs $n_seqs -culling_limit $cul -num_threads \$SLURM_NTASKS_PER_NODE -evalue $e -out ${p}-vs-nt-n$n_seqs.cul$cul.$e.blastp.out.xml

echo -e \"\\\nDONE\\\n\"
date" > run_blastn_${p}.slurm.sh
                sbatch run_blastn_${p}.slurm.sh
        done
        cd ..
done

Further Information

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

Home Application support General Training Programming support