-- ShicongXie - 08 Dec 2009
JBrowse Tutorial: Adding a Restriction Enzyme (RE) track
note: I'm running a pretty standard Ubuntu Jaunty build. jbrowse installed in /var/www/jbrowse/
Restriction Enzymes
These are enzymes that cleave RNA/DNA at specific sites. They are naturally found in bacteria, but are commonly used in the laboratory to manipulate nucleic acids in biological experiments.
tacg RE mapping tool
Run tacg (stable version 4) on your sequence. If it is not installed, use a web version hosted by UMass. I used the webversion, so the tutorial will focus on parsing the output of that program. This will generate another page of results. Now look for the text line that starts with == Match Sites by Enzyme or Pattern. Go ahead and copy that entire field into a text file.
An example line is:
BbvCI CC'TCA_GC (0 Err) - 3 Match(s) found (1.10 sites exp)
386 2505 11572
Format into GFF
I wrote a Perl script that will automatically take lines like the one above, and convert it to a GFF format for consumption by JBrowse. Use this script (perl restriction2gff.pl mysequence.fasta). The code right now will only output to output.gff (too lazy to deal with tags/error handling at the moment.)
NOTE: Go to the last few lines of the perl script and change first field (name field) of the genome on the print OUTPUT statement.
Now check your GFF output. If you'd like, cat this GFF with your existing overall GFF. Sweet! | 
