BLASTing your assembled data¶
One thing everyone wants to do is BLAST sequence data, right? Here’s a simple way to set up a stylish little BLAST server that lets you search your newly assembled sequences.
Installing blastkit¶
Installing some prerequisites:
pip install pygr
pip install whoosh
pip install git+https://github.com/ctb/pygr-draw.git
pip install git+https://github.com/ged-lab/screed.git
apt-get -y install lighttpd
and configure them:
cd /etc/lighttpd/conf-enabled
ln -fs ../conf-available/10-cgi.conf ./
echo 'cgi.assign = ( ".cgi" => "" )' >> 10-cgi.conf
echo 'index-file.names += ( "index.cgi" ) ' >> 10-cgi.conf
/etc/init.d/lighttpd restart
Next, install BLAST:
cd /root
curl -O ftp://ftp.ncbi.nih.gov/blast/executables/release/2.2.24/blast-2.2.24-x64-linux.tar.gz
tar xzf blast-2.2.24-x64-linux.tar.gz
cp blast-2.2.24/bin/* /usr/local/bin
cp -r blast-2.2.24/data /usr/local/blast-data
And put in blastkit:
cd /root
git clone https://github.com/ctb/blastkit.git -b ec2
cd blastkit/www
ln -fs $PWD /var/www/blastkit
mkdir files
chmod a+rxwt files
chmod +x /root
and run check.py:
cd /root/blastkit
python ./check.py
It should say everything is OK.
Adding the data¶
Take an assembly of interest, and copy it into /root/blaskit/db/db.fa; e.g.
cp /mnt/assembly/ecoli.21/contigs.fa /root/blastkit/db/db.fa
Formatting the database¶
After you’ve done either of the above, format and install the database for blastkit:
cd /root/blastkit
formatdb -i db/db.fa -o T -p F
python index-db.py db/db.fa
Done!
Note
You can install any file of DNA sequences you want this way; just copy it into /root/blastkit/db/db.fa and run the indexing commands, above.
Running blastkit¶
Figure out what your machine name is (ec2-???-???-???-???.compute-1.amazonaws.com) and go to:
http://machine-name/blastkit/
Make sure you have enabled port 80 in your security settings on Amazon.
...and you should see a BLAST page. If you’re searching E. coli, try:
IRHEQEAFVLHGRLQGEERETAIGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPE
GFTLLNGGPKYRRAFLDWGCFHNEPGFFTAWSNLKRLLKQRNAALRQVTRYEQLRPWDKE
LIPLAEQISTWRAEYSAGIAADMADTCKQFLPEFSLTFSFQRGWEKETEYAEVLERNFER