2) UNIX Shell Script for WNV Netblast

This is a simple shell script for using netblast on all organisms except WNV and artificial sequences to generate blast results for each WNV T-cell epitope.

WNVNetblast.sh

Process Code

for i in xx*
do
\./blastcl3 -p blastp -d nr -i $i -F F -e 200000 -I T -v 0 -b 20000 -f 11 -W 2 -T F -u "Root[ORGN] NOT txid11082[Organism:exp] NOT txid81077[ORGN]" -C F -M PAM30 -o $i.out
done



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