Tutorial: Visualise pairwise genome alignments between WBPS genomes

From release 18 (WBPS18), users can browse and visualise whole genome alignments between genomes in the same taxonomic group.

Cactus, a next-generation aligner that stores whole-genome alignments in a graph structure, was utilised to calculate multiple pairwise genome alignments between WBPS genomes. These genomes have been assigned to 5 big taxonomic groups, and pairwise alignments can be viewed between the genomes of each group.

“I would like to view how my genome of interest aligns against some related genomes”

• 1. Go to the Ensembl Genome Browser of a region of interest (example). You can do this by using the Ensembl button in the “Genome Browser” column of your genome of interest in the Genome list.
  Alternatively, if you are already on a gene page click the Region in Detail button under “Genomic Context”.

• 2. You are on the Genome Browser (Ensembl) page for your region of interest. You can click here to learn more about it.
  
• 3. Click “Configure tracks” to display the track options dialog box:

• 4. Choose the “Pairwise whole genome alignments” option of the left navigation menu in the box.

• 5. Choose the genome or multiple genomes you would like to visualise pairwise genomic alignments against. Then click the tick box at the top right of the box.
  
• 6. The genomic regions of the selected genomes that align to the region of interest appear as pink tracks on the browser. One track per genome:

• 7. You can click on the genome initials on the left of the view to view the full name of the genome each track corresponds to.

• 8. You can click on the aligned segments (pink tracks) to browse the aligned genomic region of the corresponding genome:

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