JBrowse Tutorials / Perl Scripts
Basic JBrowse Tutorials:
Formatting GenBank entries from CVS Perl script - A basic tutorial for starting to use JBrowse that addresses some the quirks of how the GFF Group field is parsed by JBrowse (Shicong Xie)
Obtaining Other Information:
We have tried to use tools available over servers on the web as much as possible to keep them accessible to more users.
GC Content - Converts the GC content of genome into WIG file. Uses a window (e.g. 5 basepairs) to generate GC content calculation. (Ashray Urs)
Restriction Enzyme Sites - How to find restriction enzyme cleavage sites and add it to JBrowse. (Shicong Xie)
Possible Primer Pairs - How to use the Primer3Plus webtool to design primers and add to JBrowse (Peerapong Pornwongthong)
Sequencing Primers for Specific Region of Interest - A script-automated tutorial of how to use Primer3Plus given a specific region in the genome; includes a parser for the output of primer manger from primer3plus. (Shicong Xie)
Glimmer gene prediction - How to use glimmer, a microbial (and viral) gene prediction software to generate gene prediction tracks. (Ashray Urs)
Multiple Align Tutorial - How to use Do Multiple Sequence Alignment by CLUSTALW and convert the file to a Jbrowse readable WIG file. (Ashray Urs)