Graphical data

The following graphical data can be added onto the map:
• Standard profiles by using the "Add standard profiles" command from the main menu or from the sequence pop-up menu. The command calls out the "Add standard profiles" dialog that allows the following selections:
  • Type of profile (*) that is to be built. To enable it, check in the checkbox near the profile name.
  • Color of profile from the drop-down list.
  • Color of data for histogram columns that are below the main axis. Colors can be selected from the "Alternate color" list.
  • Size of a window for data calculation. It can be specified in the "Window size" field.
  • Profile step in the "Step" field.
  • Profile appearance from the "Type" list: histogram or line.

Short method description. Window of user-defined size moves along the sequence by user-defined steps. In every window position, the number of appropriate nucleotides is being calculated, and the resulting profile value is obtained in accordance with certain formula:
GC Skew is calculated by formula (G - C) / (G + C).
GC Skew + (Cumulative skew) for current position is calculated as sum of all previous GC Skew values.
GC content is calculated by formula (G + C) / (A + T + G + C).
AT Skew is calculated by formula (A - T) / (A + T).
AT Skew + (Cumulative skew) for current position is calculated as sum of all previous AT Skew values.
AT content is calculated by formula (A + T) / (A + T + G + C).

• Graphic data from file using either the "Import profile from file" command from sequence pop-up menu or the "File>Import>Import profile from file" command from the main menu.

Graphical data format description

In text file, in random position, there may be a single block with graphical data.

The block beginning is marked with the string @START_PROFILES. The block is considered finished if there is the string @END_PROFILES or end of file is reached.

Block may contain data for one or more profiles. The profile data begin with the string @PROFILE <name>, where the <name> specifies the profile name. This string is mandatory.

Further, the @TYPE string specifies the type of profile, where <type> = 0 means the histogram, and <type> = 1 - line. This line is not mandatory; by default the histogram type is used.

Further, the @COLOR <color> string specifies the color of profile, where the <color> is one of standard colors (complete list of colors can be found here http://www.w3.org/TR/SVG/types.html#ColorKeywords). This line is not mandatory; by default the blue color is used.

Further, the @ALT_COLOR <color> string specifies the color of profile for histogram columns that are below the main axis, where the <color> is one of standard colors (complete list of colors can be found here http://www.w3.org/TR/SVG/types.html#ColorKeywords). This line is not mandatory; by default the basic color of profile is used.

Further, the @RANGE <start> <end> string specifies the beginning of profile data block, where the <start> specifies the starting position (numbering begins from 1) for profile, and the <end> - the ending one. This string is mandatory.

Further, the values are specified by one in a single line.

There may be multiple @RANGE blocks.