GeneQuest selects the Vienna RNA folding procedure, taken from Zuker’s optimal RNA folding method, to fold the sense strand of selected DNA regions as RNA.
To fold your region, select an area using the range selector, then select Analysis > Fold As RNA. The maximum length you may fold is 1500 bases.
At the top of the RNA folding window, GeneQuest lists the minimum energy (in Kcal/mol) of the structure, the temperature used in folding and the status of G-U pairing. To magnify or shrink the view, use the palette tools described below. The folding model is an interactive two-dimensional plot that may be saved in .ct format on both Macintosh and Windows.
Since it may take several minutes to fold your RNA, you may prefer to change the folding parameters prior to applying the method. To alter parameters before applying the method, hold down the Alt key while selecting Fold as RNA from the menu.
Two palette tools appear in the top left corner of the RNA folding window:
Zoom In
magnifies the display to 150% of the former size, letting you see more detail
but less area.
Zoom Out
reduces the display by a similar amount, letting you see the big picture while
losing some of the detail.