Genome Analysis Software Site

in silico biology, inc.

IMC F05D6 Edit Circular Content Lane of Circular Genome Map

  • Edit Circular Content Lane
  • Draw genome-specific profiles such as base composition on the Content Lane using the sliding window method.
  • In addition to the base composition, any numerical sequence created by the user can be imported and its profile can be drawn.

Operation

  1. Turn on the Content radio button in the View column of the Circular Lane Setting dialog.
  2. The Circular Content Lane setting item becomes active.
  3. Select Content
    • GC Content: Draw the GC Content profile.
    • AT Content: Draw AT Content profile.
    • GC Skew: Draw GC Skew profile.
    • AT Skew: Draw AT Skew profile.
    • Cumulative GC Skew: Draws the profile of Cumulative GC Skew.
    • Cumulative AT Skew: Draws the profile of Cumulative AT Skew.
    • Fickett: Draws a profile of gene region likeness using the Fickett method.
    • Import Data: Imports an arbitrary genome position-specific numerical sequence created by the user into Import Data and draws its profile.
  4. Set the Graph Scale.
    • Auto: If you specify Auto, the vertical scale of the profile will be set automatically.
  5. Draw the maximum profile value as the upper scale line, the minimum profile value as the lower scale line, and the average of the maximum and minimum values ​​as the center line.
    • Custom: If you specify Custom, each line of the scale can be set freely. However, Lower Line <Center Line <Upper Line.

Sliding Window Parameter setting

  • When Fixed: Fixed is specified, the window size and step size of the sliding window are set at a fixed base length regardless of the scale of the map at that time.
  • Proportional: If you specify Proportional, set the window size and step size of the sliding window as a percentage of the genome base length.

Color settings

  • Color for Lower Value below the Center Line: Set the color of the profile drawn above the center line.
  • Color for Upper Value below the Center Line: Set the color of the profile drawn below the center line.

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