BLAST

NCBI BLAST - Basic Local Alignment Search Tool

Find regions of local similarities between sequences

http://blast.ncbi.nlm.nih.gov/BlastAlign.cgi

Step 1:
Download blastn executable, blast database, and input file:
https://docs.google.com/file/d/0B12A3agEjLOMajJYUUV6WmhVWms/edit?usp=sharing


Step 2:
Move these files to folder you like. Either through command line or drag and drop.
mv ~/Downloads/blastn ~/Desktop/folderyoulike/blastn
cd ~/Desktop/folderyoulike

Step 3:
Change file permissions:
chmod 755 blastn

Step 4:
Do a blast search:
./blastn -db scaffold_6 -query ty1copia_element.fa

CENSOR

Find regions matching curated repeat elements

http://www.girinst.org/censor/index.php