blast_and_plast
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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=/db1/nr-nt-fasta-oct-2020/nt QF=yourquery.fasta plast -e 1e-10 -max-hit-per-query 1 -outfmt 1 -a $CPUs -p plastn -max-database-size 10000000000 -i $QF -d $DB -o $QF.plout -force-query-order 1000
to parse the output see http://129.173.88.134:81/dokuwiki/doku.php?id=dayana_salas_-_utility_scripts_taxonomy_coloring_trees_phylogenetics_mixture_models_domain_architecture_and_more
Here is a shell example to run BLAST:
#!/bin/bash #$ -S /bin/bash . /etc/profile #$ -cwd source activate blast export BLASTDB=/db1/nr-nt-jan-2019/ DB=nt blastn -db $DB -query yourquery.fasta -out yourqueryresults.blout source deactivate
Both shells using NCBI nt database (/db1/nr-nt-jan-2019/nt.nal), but the formats for specifying DB are different for BLAST and PLAST.
blast_and_plast.1603718664.txt.gz · Last modified: by 24.138.68.92
