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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?
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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Basics of navigating in Mauve
- 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.
- 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.
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Mauve has a useful feature to transfer the coordinates of genes across the alignment that it has made.
Other ways to
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create genome graphics
There are various powerful (non-interactive) programs
- Circos
- cgview
for drawing the awesome pictures that you see in. These tools are easiest to install Probably best installed on a computer where you have administrator privileges. They are not CPU intensive and you have to fiddle with the configuration files, so it's best to use them on your own computer where you can easily view the images that they create.
- Circos
- cgview
Evaluating eukaryotic assemblies
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