First install Blast
sudo apt-get install blast2Make a blast Directory
mkdir /home/username/blast/db cd /home/username/blast/dbconnect to blast FTP
ftp ftp.ncbi.nlm.nih.gov Connected to ftp.wip.ncbi.nlm.nih.gov. 220- Warning Notice! [ ... Extra warning message removed for brevity ... ] Name (ftp.ncbi.nlm.nih.gov:tao): anonymous 331 Anonymous login ok, send your complete email address as your password. Password: [note: enter your email address at this prompt] 230-Anonymous access granted, restrictions apply. Please read the file README.ftp 230 it was last modified on Fri Mar 28 14:05:45 2008 - 716 days ago Remote system type is UNIX. Using binary mode to transfer files.Enter Blast database directory
ftp> cd blast/dbGet a database. Below is an example and exit ftp
ftp> get 16SMicrobial.tar.gz ftp> bye 221 Goodbye.Extract the database
tar zxvpf 16SMicrobial.tar.gzEnter your query sequence in a file (q16s.txt) and execute the command below.
blastall -p blastn -i q16s.txt -d 16SMicrobial -T -o output.htmlIf you want to perform a specific organism you need to know the taxonomy id. $2 is taxonomy in below command. DB enlist the gi of of specific taxonomy to a file and the blastn is performed on specific gi list.
blastdbcmd -db 16SMicrobial -entry all -outfmt "%g %T" | \
awk ' { if ($2 == 521007) { print $1 } } ' > gilist.gi
blastn -db 16SMicrobial -query q16sF.txt -gilist gilist.gi -html -out output.html
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