Here is a shell to run **PLAST**:\\

<code>
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -o logo
#$ -cwd
#$ -pe threaded 10
cd $PWD
CPUs=10
DB=/scratch3/rogerlab_databases/other_dbs/nr_March252023/plast/nr.fasta
QF=yourquery.fasta
plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastp -max-database-size 10000000000 -i $QF -d $DB -o $QF.plout -force-query-order 1000
</code>

to parse the output see https://perun.biochem.dal.ca/user-wiki/doku.php?id=taxonomy_recovery




Here is a shell example to run **BLAST**:\\

<code>
#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -pe threaded 10
#$ -cwd
source activate blast
export BLASTDB=/db1/blast-may-2024/
DB=nt
query=your_query.fasta
blastn -db $DB -query $query -out yourqueryresults.blout -num_threads 10 -outfmt "6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle"
conda deactivate
</code>

Both shells use NCBI nt database, but PLAST doesn't support new v5 NCBI nr and nt databases and can cause Segmentation fault error.

<Last updated by Dandan Zhao on Jun 11, 2024>