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3.4 Energy dot plot parameter selection

The user is prompted for three parameters. The first is the ``minimum vector size for plot''. This parameter controls the clutter on the display screen. Only helical regions that contain at least this number of consecutive base pairs will be plotted as points. The default is 1; that is, to plot every base pair within a user selected energy increment from the minimum.

The user is then prompted for the ``window size''. This parameter can also be regarded as 1 less than the minimum ``distance'' between any two predicted foldings [23]. When a base pair has been selected from the screen and an (otherwise) optimal structure containing that base pair has been computed, the program marks all the base pairs in the computed structure as well as any base pairs that are within a ``window size'' distance from these base pairs.
In an RNA molecule r<sub>i</sub> ,r<sub>i+1</sub> , ... ,r<sub>n</sub>, the distance between two base pairs r<sub>i</sub>-r<sub>j</sub> and r<sub>i′</sub>-r<sub>j′</sub> is defined to be max{|i-i′|,|j-j′|}
When the energy dot plot is redrawn, the marked base pairs do not appear. This gives the user a chance to select a base pair that is not ``too close'' to any base pairs that have already occurred in computed foldings. In addition, subsequent computed foldings will not be output unless they contain at least ``window size'' unmarked base pairs. The choice of the window parameter is discussed in 3.5. If one's aim is merely to look at the dot plot and see which structural features are ``well defined'', with few competing structures, then the value of this parameter is irrelevant.

In a continuation run, program execution continues with input save file name selection (3.7). Otherwise, in a regular run, program execution continues with sequence file name selection (3.6).

Michael Zuker
Thu Nov 2 14:28:14 CST 1995