Visualizing assemblies using Mauve
Mauve uses a fast sequence matching algorithm to identify Locally Collinear Blocks (LCBs) between genomes. It has a really slick interface for viewing whole genome alignments or of viewing your genome assembly aligned to a closely related species.
Install Mauve
On your Desktop (local) machine. Go here in a web browser:
Choose Linux (it's ok to leave the other boxes blank).
Mauve has a binary that you should be able to launch by double-clicking on it.
Download Data
In a terminal on your Desktop (local) machine.
scp -r username@tacc.utexas.edu:/corral-repl/utexas/BioITeam/ngs_course/mauve_examples ~/Desktop
Example: Comparing two whole genomes
First we're just going to view two related species versus one another.
Choose: File → Align with progressiveMauve.
Navigate to the mauve_examples folder that you downloaded and choose:
NC_000913.2.gbkNC_004631.1.gbk
Then hit the Align... button. Choose to save the result as genome_alignment_result or something similar.
A console window will pop up and show a bunch of commands that are being run at the command line for you. You could run them yourself at the terminal if you wanted to use Mauve on Lonestar or another machine in power-user mode.
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."
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.
Example: Comparing assemblies to a reference genome
Next, we are going to compare several assemblies that were created in.
Choose: Tools → Move Contigs...
Navigate to the mauve_examples folder that you downloaded and choose:
NC_000913.2.gbkpairedc20.fapairedc25.fapairedc50.fa
Transferring annotation
Mauve has a useful feature to transfer the coordinates of genes across the alignment that it has made. This can be a good way of assigning orthologs.
Choose: Tools → Export... → Export Orthologs
Other ways to create genome graphics
There are various powerful (non-interactive) programs for drawing the awesome pictures that you see in. These tools are easiest to install 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 - fully featured. Very cool functions for drawing connections between different chromosome locations.
- CGView Simpler to use. Better functionality for showing genes up close as arrows. Does not draw links.
Evaluating eukaryotic assemblies
If you are going to seriously annotate a eukaryotic genome, then you are going to need a machine with database infrastructure and other tools installed. Here are two systems for annotating gene structure in eukaryotic genomes:
PASA - Program to Assemble Spliced Alignments
CEGMA - Core Eukaryotic Genes Mapping Approach