Understanding RNA folding energy dot-plots

This short video describes how to walk through a DNA or RNA sequence dot plot and generate a 2D RNA fold structure. It discusses the theoretical nature of these structures, environmental conditions that can effect them, and alternative structural configurations. This video is provided as supplemental information for the 2015 Biovis Data Analysis contest. For more information, see the Design, and Data Analysis contests at biovis.net/
Additional details you should know:
* For a better understanding of the precise meaning of dots, and similarly or differently colored dots in a dot-plot, see the mfold documentation here : mfold.rna.albany.edu/doc/mfold...
* The base-pairings mentioned in the video -- G-C, and A-T (DNA) or A-U (RNA) -- are canonical "Watson-Crick" base pairs. Some other "Non Watson-Crick" base pairings are possible, for example G-T or U. These are typically less energetically favorable than the Watson-Crick pairings, but, just as different environmental factors like other molecules in the solution can pressure an RNA structure away from the naive in-isolation optimum, individually-less-than-optimal base-pairings may be used by nature, if that pairing optimizes the whole-system energetics. You can begin to get a sense of other pairing possibilities from WikiPedia's page on Wobble base pairs en.wikipedia.org/wiki/Wobble_b... however, additional possibilities do exist.
* The question of comparing structures is more complex than simply comparing structures: It's entirely possible for two RNA molecules to have the exact same set of possible structures, yet function differently in the cell - for example, if the energies associated with the different structures are different between the molecules, predisposing the molecules towards different regions of their shared structure space.