visualize progressive mauve alignments

[phbrito]

Hello,
I would like to know if there is any tool installed to visualize progressive mauve alignments.
Thanks

[jennaj]

Hi @phbrito

Good question! There are a few options now, and potentially more soon.

1. The CPT public Galaxy server hosts a visualization tool. If you run progressiveMauve in Galaxy, the gff3 and mxfa output will be created, but you’ll need to provide the reference genome fasta yourself from the history (none are natively indexed).

• Tool: https://cpt.tamu.edu/galaxy-pub/root?tool_id=edu.tamu.cpt.comparative.mauve
• Galaxy Platform Directory page with contact information, including how to request more space: https://galaxyproject.org/use/center-for-phage-technology-cpt/
• How to format custom reference genomes used “from the history”. The primary goal is to ensure that the chromosome identifiers “match up” between all inputs:
  • Preparing and using a Custom Reference Genome or Build
  • Mismatched Chromosome identifiers (and how to avoid them)

2. None of the usegalaxy.* servers incorporate that tool (yet). This is now under consideration. We will likely know more by mid-next week. Feel free to write back after then for an update if we don’t write back here first.

3. Those options are fine, but installing and using the Mauve browser directly is definitely an alternative for full visualization functionality specifically designed to work with these data (whether created directly with Mauve or in the Galaxy wrapped version). Find it here: http://darlinglab.org/mauve/user-guide/installing.html

Hope that helps!

Ps: Thank you @hexylena for assistance and clarification for all of the above!!

[hexylena]

Hi @phbrito,

I’ve placed the tool on the usegalaxy.eu (maybe easier to use; much more popular/more tools/well maintained/bigger quota)

Here is an example history where you can see the output. This was written by Eleni Mijalis at the CPT. It worked well enough for our purposes, basic structural rearrangement visualisation, but it is not being actively developed.

The X-Vis tool takes the XMFA file and a GFF3 file showing annotations, and visualises it:

Each contig is placed vertically, the blue boxes represent an LCB region, and the grey lines connect them. All features from the gff3 are visualised as black arrow boxes.

1. Clicking on a black feature will show the feature name at the bottom
2. Double clicking a blue LCB box will re-align the visualisation to center those LCBs across all contigs
3. You can scroll vertically to zoom in on a single region
4. Click and drag to pan around.

Mauve is more full featured, but, this was a convenient way to include it into our comparative genomics workflows