Genome Analysis Software Site

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IMC W521A DotPlot Execution Dialog Items Explained

Description of the DotPlot execution dialog.

In the list box at the top, all the genome sequences loaded in the current reference directory are displayed.

The items of each line are as follows.

Select radio button: The genomic sequence turned on is compared with the genomic sequence of the main feature map and the selected genome is displayed as the Y axis.

Genome shape: The genomic sequence is linear or circular.

Name: Displays the file name of the genome sequence.

Length: Displays the total base length of the genome sequence.


In the lower list box, specify the condition and color for determining the fill color of each dot.

Each dot judges the top condition, fills with the fill color if it is satisfied, and judges the condition immediately below if it does not.

There are two kinds of conditions as below, AND of each is judged.

Overlap Length input field: Since this value is usually 1 (100%), designation of any numerical value has no effect on judgment.

% Identigy input field: Specifies the percentage of matching bases between two segments.

Fill color box: You can change the fill color by clicking the box.


Run button: Click to execute DotPlot.

Close button: When clicked, DotPlot will not be executed and the dialog will close.

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