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.

• Mauve Web site

Download Mauve

On your Desktop (local) machine. Go here in a web browser:

• Mauve download page

Choose Linux (it's ok to leave the other boxes blank).

Download Data

In a terminal on your Desktop (local) machine.

cd ~/Desktop
scp -r username@tacc.utexas.edu:

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_data folder that you downloaded and choose:

• NC_000913.2.gbk
• NC_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

Navigating in Mauve

• You can move around and zoon 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.

What do the

Example: Comparing an assembly to a reference genome

Transferring annotation

Mauve has a useful feature to transfer the coordinates of genes across the alignment that it has made.

Other ways to creating genome graphics

There are various powerful (non-interactive) programs

• Circos
• cgview

These tools are easiest to install Probably best installed

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