vision_board.txt

I want this version of domesticator to be a little more structure-aware than previous versions. This means both in terms of RNA structure as well as protein structure.

This means 
1) making it compatible with naturalizer, whenever that happens
2) Learn viennaRNA and use it to optimize RNA structure

I also want to change up how I do the optimization. dnachisel is fast, so I could do several
rounds of optimization and pick the best one as suggested by several ppl in baker lab.

Finally I want to make more use of genbank files for easier record keeping and easier optimization of complicated genes (e.g. multicistronic transcripts)

Let's start from scratch with the latest release of dnachisel

consider switching the name to DeNovatello or Michelangeneo, to make a stupid pun making reference to the fact that the underlying optimization library is dnachisel

Good datasets here for preventing unintended binding sites: http://regulondb.ccg.unam.mx/central_panel_menu/downloads_menu.jsp