• Profile plotting
  • Profile plotting is displayed in graphic windows. This section explains how to handle the plot.

    DNAMAN may illustrate the properties of DNA or protein molecules in a graphic window by plotting the property values against the positions. The results of three functions are shown in profile plotting window: 1) DNA thermodynamic properties, 2) Protein hydrophobic/hydrophilic profiles, and 3) Protein secondary structure profiles.

    The plot is presented in a rectangle with the property values as ordinate and positions as abscissa. When you place the cursor (cross shape) on the plot, the current property value and position are displayed on the left corner of the screen (Status bar). In addition to the tools described in the above sections for handling a graphic window, the following tools allow you to perform more detailed analyses on the profiles.

    1) Graphic positions

    You may move the plot positions within the graphic window. Place the cursor on the up-left corner of the plot. When the cursor switches to Cross, press and hold the left mouse button and drag the plot.

    2) Graphic sizes

    You may change the size and shape of the plot. Place the cursor on the low-right corner of the plot. When the cursor switches to , press and hold the left mouse button and drag the plot to desired size and shape.

    3) End positions

    There are four buttons on the top of the graphic window. The third and fourth buttons control the end positions of the plot. To change the left end, you may press the third button then enter a Start position in the text box. You may also press the thumb beside the button to increase or decrease the number. Use the same method to changes the right position of the plot by operating the fourth button.

    4) Export data

    You may export the plot data to a text file by pressing the Export (second) button. DNAMAN lists all plotting data in a table. You may save the table in a file and import it to other graphic/table programs such as Microsoft Excel.

    5) Options

    You may modify the properties of the plot by pressing the Options button.

    In the Options dialog box, DNAMAN lists all sets of data in the plot. You may check or remove any of the sets for display in the plot.

    The Window Size parameter is used to average the property values. Increasing the Window Size may smooth the profile. If the size is 1, the profile represents the exact property value of each position. If the size is greater than 1, DNAMAN will repetitively average the property values for each position in the plot.

    You may change the scale of ordinate by defining the values of Scale from and to (Y-Scale).