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3.11.4 Displaying the ``P-num plot''

The P-Num plot plots the total number of dots in the ith row and jth column of the dot plot array (ordinate) versus the historical numbering for i (abscissa). For the ith base in the fragment, P-Num(i) is the total number of different base pairs that can be formed with the ith base in all possible foldings within the selected energy increment. The P-Num plot is intended to give a rough idea of what parts of the RNA sequence have a ``well-determined'' structure. It is not as effective as looking at the dot plot, and no ``hard copy'' option is available for the P-Num plot in the program as distributed.

The P-Num plot can be toggled on and off by selecting the ``Toggle pnumplot'' item from the popup menu.

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