Whole genome alignments, Demo

Demo: Whole-genome alignments

Alignments in the Region in Detail view

Let’s look at some of the comparative genomics views in the Location tab. Go to the region 4:4:4640000-4680000 in Coffea canephora (coffee). We can look at individual species comparative genomics tracks in this view by clicking on Configure this page.

Select Comparative genomics from the left-hand menu to choose alignments between closely related species. Turn on the alignments for Arabidopsis thaliana, Oryza sativa japonica Group (rice) and Solanum lycopersicum (tomato).

Sequence alignments

We can also look at the alignment between species or groups of species as text. Click on Comparative Genomics: Alignments (text) in the left-hand menu.

Click on Select an alignment to open the alignment menu. Select A. thaliana from the alignments list then click Go.

In this case there are 12 blocks aligned of different lengths. Click on Block 1.

You will see a list of the regions aligned, followed by the sequence alignment. Click on Display full alignment. Exons are shown in red (you may need to scroll down the page to see the first exon).

Region comparison

To compare with both contigs visually, go to Comparative Genomics: Region Comparison.

To add species to this view, click on the green Select species or regions button. Choose A. thaliana again then close the menu.

Synteny

We can view large-scale syntenic regions from our chromosome of interest. Click on Comparative Genomics: Synteny in the left-hand menu and select S. lycopersicum* from the **Change species drop-down in the right-hand side.

Black linking lines indicate sequences are oriented in the same directed, red linking lines indicate the sequences are inverted.