I''d like to understand the pairing probability dot plots provided in the RNA Lab. The Lab Manual says,

"The lower half triangle of the plot only colors pairs that are in the minimum free energy structure."

Is the "minimum free energy structure" the same as the targeted design shape? Is it correct that the lower left triangle only shows which bases in the design shape have paired with each other? This seems to be independent of the precise sequence of bases. We are given the shape before any bases have even been specified.

Googling this suggests that there is a certain amount of freedom in how dot plots can be generated, depending on what you're looking at. Is there a more detailed description somewhere of how the upper right triangle of our plot is calculated? This seems to depend on the precise sequence of bases, and allowing the shape to vary. (am i right?)

Tim (Ogrelike)

"The lower half triangle of the plot only colors pairs that are in the minimum free energy structure."

Is the "minimum free energy structure" the same as the targeted design shape? Is it correct that the lower left triangle only shows which bases in the design shape have paired with each other? This seems to be independent of the precise sequence of bases. We are given the shape before any bases have even been specified.

Googling this suggests that there is a certain amount of freedom in how dot plots can be generated, depending on what you're looking at. Is there a more detailed description somewhere of how the upper right triangle of our plot is calculated? This seems to depend on the precise sequence of bases, and allowing the shape to vary. (am i right?)

Tim (Ogrelike)