3) UNIX Shell Script for HIV Standalone Blast

This is a simple script for using standalone blast against the HIV database to generate blast results for each HIV T-cell epitope.


HIVstandaloneblast.sh

Process Code

for i in xx*
do
blastall -p blastp -d HIV_db1.fasta -i $i -F F -e 200000 -I T -v 0 -b 20000 -f 11 -W 2 -T F -C F -M PAM30 -o $i.out
done



Code by: BenBen & Asif M. Khan
Blog Post by: BenBen
Post Edited by: BenBen