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After a little bit, a window will pop up showing the aligned genomes. It should look something like this:
What's going on?
Form From the Mauve manual:
"When a block lies above the center line the aligned region is in the forward orientation relative to the first genome sequence. Blocks below the center line indicate regions that align in the reverse complement (inverse) orientation. Regions outside blocks lack detectable homology among the input genomes. Inside each block Mauve draws a similarity profile of the genome sequence. The height of the similarity profile corresponds to the average level of conservation in that region of the genome sequence. Areas that are completely white were not aligned and probably contain sequence elements specific to a particular genome."
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- You can move around and zoom in and out using control and the arrow keys.
- You can click on a region in one genome to center the aligned regions in the other genome to it.
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- You can switch which genome is the main reference by clicking on the up and down arrows on the left side.
- If you zoom in far enough, sequence features (genes) will show up.
Example: Comparing
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assemblies to a reference genome
Transferring annotation
Mauve has a useful feature to transfer the coordinates of genes across the alignment that it has made.
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