Genome Analysis Software Site

in silico biology, inc.

IMC O10A Operation of Gene Cluster Alignement

Preparation

Load the closely related genome sequence (CDS must be annotated) to be compared into the current reference directory.

Load one genome into the current main directory.

Operation

Identify the gene of interest (CDS) on the main feature map using keyword search etc.

We will do keyword search here. Select Search -> Keyword Search ... from the menu.

The Keyword Search dialog will be displayed. 

Check the feature key CDS and enter the search keyword (here hisG) in the Keyword (s) text field.

Click "Run".

The Keyword Search Result dialog is displayed.

When you check the list, the CDS will be displayed in the center of the main feature map.

Right-click on the CDS feature searched.

A pull-down menu will be displayed.

Select Show Homology -> Show Homology A.A.

Homology search is executed. 

When the search is completed, the Homology Search hit list dialog will be displayed.

Click each line in the dialog.

Each genome of the reference feature map is aligned around homologous CDS.

Right-click on the CDS where the reference feature map lined up.

A pull-down menu will be displayed.

Select Gene Cluster Alignment ....

The Gene Cluster Alignment Setting dialog is displayed.

Click "Set".

An execution confirmation message is displayed.

Click "Yes (Y)".

Execution is started and a progress message is displayed during execution.

When execution is completed, the Binary Best Hit (BBH) List dialog box is displayed, and at the same time, bands showing homology are displayed between genomes of related genomes in the reference feature map.

In this state, use the zoom feature of the reference feature map or the scroll button to manipulate the map.

Also, clicking on each line of the BBH List dialog will highlight the homology-related CDS and binding band indicated by that line.

Below is the zoomed out view of the reference feature map.

Below is the click of the line of the BBH list. The part corresponding to the clicked line is highlighted.

Below is the side scroll of the bottom genome.

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