cgeb2001's DokuWiki!

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Here is a shell to run PLAST:

#!/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

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:

#!/bin/bash
#$ -S /bin/bash
. /etc/profile
#$ -pe threaded 1
#$ -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 1 -outfmt "6 qseqid sseqid evalue pident qcovs length slen qlen qstart qend sstart send stitle"
source deactivate

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