4. Get Genome Alignment Data and Visualization Result

Click button "Structure Analysis" in PGAP-X Lite Launcher, you will get the "Structure Analysis" interface like Figure 4.0.1. Including three functional buttons:

Figure 3.1.1 miss
Figuer 4.0.1: The Three functional buttons in Genome Alignment part.
The Third button "Visualize Genome Alignment Result" will only be available when there is alignment result in your workspace.

4.4. Get Genome Alignment Visualization Result

  Genome alignment result is in the form of high conserved blocks in genomes, during visualization,we get the information of each block from alignment result, and then according to the site of genome, we draw each block in genome, and different aligned block will be in different color. Each colored line stand for a single genome, and one colored segment stands for one block with one color.

  You can get your visualization result in two ways: either choose "Ok" when finishing alignment, or click "Genome Alignment Result Visualization" button in Genome Alignment interface(Figure 4.0.1). And Figure 4.4.1 is the visualization result of my genome alignment data.

Figure 4.4.1 miss
Figuer 4.4.1: Genome alignment visualization

  You can save your visualization into JPG image file, or SVG file, by clicking the menu part of "File".

4.5. User Interaction in Genome Alignment Visualization

  We develop many user interacting functions in out tool.

  The first interacting function is you can choose which genome to display, and set genome order, by clicking the menu part of "Edit"-->"Genome List". Figure 4.5.1 shows the interface window that can change genomes and order.

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Figuer 4.5.1: Change genome list and order

  Here we just choose three genomes and change their order:NC_012467, NC_014498 and NC_014494. We can see the result in Figure 4.5.2.

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Figuer 4.5.2: Visualization result after changing genome list and order

  The second interacting function is that you can align the genome by nucleotide site, by double clicking a site with your mouse. In Figure 4.5.3 , we double click a purple site in genome NC_014251.

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Figuer 4.5.3: Visualization result after double clicking a specific site.

  The third interacting function is toolbar, you can zoom in, zoom out, move right, move left, and go back to the initial state.

Go to initial state
Zoom in
Zoom out
Move left
Move right

  Figure 4.5.4 shows a visualization result of zoom in.

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Figuer 4.5.4: Visualization result after zoom in.